New Insights Into the Role of mTOR Signaling in the Cardiovascular System.
Sciarretta Sebastiano,Forte Maurizio,Frati Giacomo,Sadoshima Junichi
Circulation research
The mTOR (mechanistic target of rapamycin) is a master regulator of several crucial cellular processes, including protein synthesis, cellular growth, proliferation, autophagy, lysosomal function, and cell metabolism. mTOR interacts with specific adaptor proteins to form 2 multiprotein complexes, called mTORC1 (mTOR complex 1) and mTORC2 (mTOR complex 2). In the cardiovascular system, the mTOR pathway regulates both physiological and pathological processes in the heart. It is needed for embryonic cardiovascular development and for maintaining cardiac homeostasis in postnatal life. Studies involving mTOR loss-of-function models revealed that mTORC1 activation is indispensable for the development of adaptive cardiac hypertrophy in response to mechanical overload. mTORC2 is also required for normal cardiac physiology and ensures cardiomyocyte survival in response to pressure overload. However, partial genetic or pharmacological inhibition of mTORC1 reduces cardiac remodeling and heart failure in response to pressure overload and chronic myocardial infarction. In addition, mTORC1 blockade reduces cardiac derangements induced by genetic and metabolic disorders and has been reported to extend life span in mice. These studies suggest that pharmacological targeting of mTOR may represent a therapeutic strategy to confer cardioprotection, although clinical evidence in support of this notion is still scarce. This review summarizes and discusses the new evidence on the pathophysiological role of mTOR signaling in the cardiovascular system.
10.1161/CIRCRESAHA.117.311147
Transcriptional regulation of the cardiac conduction system.
van Eif Vincent W W,Devalla Harsha D,Boink Gerard J J,Christoffels Vincent M
Nature reviews. Cardiology
The rate and rhythm of heart muscle contractions are coordinated by the cardiac conduction system (CCS), a generic term for a collection of different specialized muscular tissues within the heart. The CCS components initiate the electrical impulse at the sinoatrial node, propagate it from atria to ventricles via the atrioventricular node and bundle branches, and distribute it to the ventricular muscle mass via the Purkinje fibre network. The CCS thereby controls the rate and rhythm of alternating contractions of the atria and ventricles. CCS function is well conserved across vertebrates from fish to mammals, although particular specialized aspects of CCS function are found only in endotherms (mammals and birds). The development and homeostasis of the CCS involves transcriptional and regulatory networks that act in an embryonic-stage-dependent, tissue-dependent, and dose-dependent manner. This Review describes emerging data from animal studies, stem cell models, and genome-wide association studies that have provided novel insights into the transcriptional networks underlying CCS formation and function. How these insights can be applied to develop disease models and therapies is also discussed.
10.1038/s41569-018-0031-y
Human pluripotent stem cells: Prospects and challenges as a source of cardiomyocytes for in vitro modeling and cell-based cardiac repair.
Hartman Matthew E,Dai Dao-Fu,Laflamme Michael A
Advanced drug delivery reviews
Human pluripotent stem cells (PSCs) represent an attractive source of cardiomyocytes with potential applications including disease modeling, drug discovery and safety screening, and novel cell-based cardiac therapies. Insights from embryology have contributed to the development of efficient, reliable methods capable of generating large quantities of human PSC-cardiomyocytes with cardiac purities ranging up to 90%. However, for human PSCs to meet their full potential, the field must identify methods to generate cardiomyocyte populations that are uniform in subtype (e.g. homogeneous ventricular cardiomyocytes) and have more mature structural and functional properties. For in vivo applications, cardiomyocyte production must be highly scalable and clinical grade, and we will need to overcome challenges including graft cell death, immune rejection, arrhythmogenesis, and tumorigenic potential. Here we discuss the types of human PSCs, commonly used methods to guide their differentiation into cardiomyocytes, the phenotype of the resultant cardiomyocytes, and the remaining obstacles to their successful translation.
10.1016/j.addr.2015.05.004
Modeling Development and Disease with Organoids.
Clevers Hans
Cell
Recent advances in 3D culture technology allow embryonic and adult mammalian stem cells to exhibit their remarkable self-organizing properties, and the resulting organoids reflect key structural and functional properties of organs such as kidney, lung, gut, brain and retina. Organoid technology can therefore be used to model human organ development and various human pathologies 'in a dish." Additionally, patient-derived organoids hold promise to predict drug response in a personalized fashion. Organoids open up new avenues for regenerative medicine and, in combination with editing technology, for gene therapy. The many potential applications of this technology are only beginning to be explored.
10.1016/j.cell.2016.05.082
Human induced pluripotent stem cells for modelling neurodevelopmental disorders.
Ardhanareeswaran Karthikeyan,Mariani Jessica,Coppola Gianfilippo,Abyzov Alexej,Vaccarino Flora M
Nature reviews. Neurology
We currently have a poor understanding of the pathogenesis of neurodevelopmental disorders, owing to the fact that postmortem and imaging studies can only measure the postnatal status quo and offer little insight into the processes that give rise to the observed outcomes. Human induced pluripotent stem cells (hiPSCs) should, in principle, prove powerful for elucidating the pathways that give rise to neurodevelopmental disorders. hiPSCs are embryonic-stem-cell-like cells that can be derived from somatic cells. They retain the unique genetic signature of the individual from whom they were derived, and thus enable researchers to recapitulate that individual's idiosyncratic neural development in a dish. In the case of individuals with disease, we can re-enact the disease-altered trajectory of brain development and examine how and why phenotypic and molecular abnormalities arise in these diseased brains. Here, we review hiPSC biology and possible experimental designs when using hiPSCs to model disease. We then discuss existing hiPSC models of neurodevelopmental disorders. Our hope is that, as some studies have already shown, hiPSCs will illuminate the pathophysiology of developmental disorders of the CNS and lead to therapeutic options for the millions that are affected by these conditions.
10.1038/nrneurol.2017.45
Transient receptor potential channels in cardiac health and disease.
Hof Thomas,Chaigne Sébastien,Récalde Alice,Sallé Laurent,Brette Fabien,Guinamard Romain
Nature reviews. Cardiology
Transient receptor potential (TRP) channels are nonselective cationic channels that are generally Ca permeable and have a heterogeneous expression in the heart. In the myocardium, TRP channels participate in several physiological functions, such as modulation of action potential waveform, pacemaking, conduction, inotropy, lusitropy, Ca and Mg handling, store-operated Ca entry, embryonic development, mitochondrial function and adaptive remodelling. Moreover, TRP channels are also involved in various pathological mechanisms, such as arrhythmias, ischaemia-reperfusion injuries, Ca-handling defects, fibrosis, maladaptive remodelling, inherited cardiopathies and cell death. In this Review, we present the current knowledge of the roles of TRP channels in different cardiac regions (sinus node, atria, ventricles and Purkinje fibres) and cells types (cardiomyocytes and fibroblasts) and discuss their contribution to pathophysiological mechanisms, which will help to identify the best candidates for new therapeutic targets among the cardiac TRP family.
10.1038/s41569-018-0145-2
Reassembling embryos in vitro from component stem cells.
Cell research
Researchers at the University of Cambridge, UK have succeeded in reconstructing mouse embryos by combining pluripotent embryonic and multipotent trophoblast stem cells in a 3D scaffold; the study from the laboratory of Professor Zernicka-Goetz, recently published in Science, provides a break-through tool to probe early mammalian development outside the uterus. Achieving a similar feat with human cells might necessitate reconsideration of the 14-day rule as a limitation of such research.
10.1038/cr.2017.61
Endocardial Notch Signaling in Cardiac Development and Disease.
Luxán Guillermo,D'Amato Gaetano,MacGrogan Donal,de la Pompa José Luis
Circulation research
The Notch signaling pathway is an ancient and highly conserved signaling pathway that controls cell fate specification and tissue patterning in the embryo and in the adult. Region-specific endocardial Notch activity regulates heart morphogenesis through the interaction with multiple myocardial-, epicardial-, and neural crest-derived signals. Mutations in NOTCH signaling elements cause congenital heart disease in humans and mice, demonstrating its essential role in cardiac development. Studies in model systems have provided mechanistic understanding of Notch function in cardiac development, congenital heart disease, and heart regeneration. Notch patterns the embryonic endocardium into prospective territories for valve and chamber formation, and later regulates the signaling processes leading to outflow tract and valve morphogenesis and ventricular trabeculae compaction. Alterations in NOTCH signaling in the endocardium result in congenital structural malformations that can lead to disease in the neonate and adult heart.
10.1161/CIRCRESAHA.115.305350
Ovarian Follicular Theca Cell Recruitment, Differentiation, and Impact on Fertility: 2017 Update.
Endocrine reviews
The major goal of this review is to summarize recent exciting findings that have been published within the past 10 years that, to our knowledge, have not been presented in detail in previous reviews and that may impact altered follicular development in polycystic ovarian syndrome (PCOS) and premature ovarian failure in women. Specifically, we will cover the following: (1) mouse models that have led to discovery of the derivation of two precursor populations of theca cells in the embryonic gonad; (2) the key roles of the oocyte-derived factor growth differentiation factor 9 on the hedgehog (HH) signaling pathway and theca cell functions; and (3) the impact of the HH pathway on both the specification of theca endocrine cells and theca fibroblast and smooth muscle cells in developing follicles. We will also discuss the following: (1) other signaling pathways that impact the differentiation of theca cells, not only luteinizing hormone but also insulinlike 3, bone morphogenic proteins, the circadian clock genes, androgens, and estrogens; and (2) theca-associated vascular, immune, and fibroblast cells, as well as the cytokines and matrix factors that play key roles in follicle growth. Lastly, we will integrate what is known about theca cells from mouse models, human-derived theca cell lines from patients who have PCOS and patients who do not have PCOS, and microarray analyses of human and bovine theca to understand what pathways and factors contribute to follicle growth as well as to the abnormal function of theca.
10.1210/er.2017-00164
Stem Cells: A Renaissance in Human Biology Research.
Wu Jun,Izpisua Belmonte Juan Carlos
Cell
The understanding of human biology and how it relates to that of other species represents an ancient quest. Limited access to human material, particularly during early development, has restricted researchers to only scratching the surface of this inherently challenging subject. Recent technological innovations, such as single cell "omics" and human stem cell derivation, have now greatly accelerated our ability to gain insights into uniquely human biology. The opportunities afforded to delve molecularly into scarce material and to model human embryogenesis and pathophysiological processes are leading to new insights of human development and are changing our understanding of disease and choice of therapy options.
10.1016/j.cell.2016.05.043
Human germ cell tumours from a developmental perspective.
Nature reviews. Cancer
Human germ cell tumours (GCTs) are derived from stem cells of the early embryo and the germ line. They occur in the gonads (ovaries and testes) and also in extragonadal sites, where migrating primordial germ cells are located during embryogenesis. This group of heterogeneous neoplasms is unique in that their developmental potential is in effect determined by the latent potency state of their cells of origin, which are reprogrammed to omnipotent, totipotent or pluripotent stem cells. Seven GCT types, defined according to their developmental potential, have been identified, each with distinct epidemiological and (epi)genomic features. Heritable predisposition factors affecting the cells of origin and their niches likely explain bilateral, multiple and familial occurrences of the different types of GCTs. Unlike most other tumour types, GCTs are rarely caused by somatic driver mutations, but arise through failure to control the latent developmental potential of their cells of origin, resulting in their reprogramming. Consistent with their non-mutational origin, even the malignant tumours of the group are characterized by wild-type TP53 and high sensitivity for DNA damage. However, tumour progression and the rare occurrence of treatment resistance are driven by embryonic epigenetic state, specific (sub)chromosomal imbalances and somatic mutations. Thus, recent progress in understanding GCT biology supports a comprehensive developmental pathogenetic model for the origin of all GCTs, and provides new biomarkers, as well as potential targets for treatment of resistant disease.
10.1038/s41568-019-0178-9
Deconstructing and reconstructing the mouse and human early embryo.
Shahbazi Marta N,Zernicka-Goetz Magdalena
Nature cell biology
The emergence of form and function during mammalian embryogenesis is a complex process that involves multiple regulatory levels. The foundations of the body plan are laid throughout the first days of post-implantation development as embryonic stem cells undergo symmetry breaking and initiate lineage specification, in a process that coincides with a global morphological reorganization of the embryo. Here, we review experimental models and how they have shaped our current understanding of the post-implantation mammalian embryo.
10.1038/s41556-018-0144-x
Endothelial to Mesenchymal Transition: Role in Physiology and in the Pathogenesis of Human Diseases.
Piera-Velazquez Sonsoles,Jimenez Sergio A
Physiological reviews
Numerous studies have demonstrated that endothelial cells are capable of undergoing endothelial to mesenchymal transition (EndMT), a newly recognized type of cellular transdifferentiation. EndMT is a complex biological process in which endothelial cells adopt a mesenchymal phenotype displaying typical mesenchymal cell morphology and functions, including the acquisition of cellular motility and contractile properties. Endothelial cells undergoing EndMT lose the expression of endothelial cell-specific proteins such as CD31/platelet-endothelial cell adhesion molecule, von Willebrand factor, and vascular-endothelial cadherin and initiate the expression of mesenchymal cell-specific genes and the production of their encoded proteins including α-smooth muscle actin, extra domain A fibronectin, N-cadherin, vimentin, fibroblast specific protein-1, also known as S100A4 protein, and fibrillar type I and type III collagens. Transforming growth factor-β1 is considered the main EndMT inducer. However, EndMT involves numerous molecular and signaling pathways that are triggered and modulated by multiple and often redundant mechanisms depending on the specific cellular context and on the physiological or pathological status of the cells. EndMT participates in highly important embryonic development processes, as well as in the pathogenesis of numerous genetically determined and acquired human diseases including malignant, vascular, inflammatory, and fibrotic disorders. Despite intensive investigation, many aspects of EndMT remain to be elucidated. The identification of molecules and regulatory pathways involved in EndMT and the discovery of specific EndMT inhibitors should provide novel therapeutic approaches for various human disorders mediated by EndMT.
10.1152/physrev.00021.2018
At the Crossroads of Fate-Somatic Cell Lineage Specification in the Fetal Gonad.
Rotgers Emmi,Jørgensen Anne,Yao Humphrey Hung-Chang
Endocrine reviews
The reproductive endocrine systems are vastly different between males and females. This sexual dimorphism of the endocrine milieu originates from sex-specific differentiation of the somatic cells in the gonads during fetal life. Most gonadal somatic cells arise from the adrenogonadal primordium. After separation of the adrenal and gonadal primordia, the gonadal somatic cells initiate sex-specific differentiation during gonadal sex determination with the specification of the supporting cell lineages: Sertoli cells in the testis vs granulosa cells in the ovary. The supporting cell lineages then facilitate the differentiation of the steroidogenic cell lineages, Leydig cells in the testis and theca cells in the ovary. Proper differentiation of these cell types defines the somatic cell environment that is essential for germ cell development, hormone production, and establishment of the reproductive tracts. Impairment of lineage specification and function of gonadal somatic cells can lead to disorders of sexual development (DSDs) in humans. Human DSDs and processes for gonadal development have been successfully modeled using genetically modified mouse models. In this review, we focus on the fate decision processes from the initial stage of formation of the adrenogonadal primordium in the embryo to the maintenance of the somatic cell identities in the gonads when they become fully differentiated in adulthood.
10.1210/er.2018-00010
The role of 3D genome organization in development and cell differentiation.
Zheng Hui,Xie Wei
Nature reviews. Molecular cell biology
In eukaryotes, the genome does not exist as a linear molecule but instead is hierarchically packaged inside the nucleus. This complex genome organization includes multiscale structural units of chromosome territories, compartments, topologically associating domains, which are often demarcated by architectural proteins such as CTCF and cohesin, and chromatin loops. The 3D organization of chromatin modulates biological processes such as transcription, DNA replication, cell division and meiosis, which are crucial for cell differentiation and animal development. In this Review, we discuss recent progress in our understanding of the general principles of chromatin folding, its regulation and its functions in mammalian development. Specifically, we discuss the dynamics of 3D chromatin and genome organization during gametogenesis, embryonic development, lineage commitment and stem cell differentiation, and focus on the functions of chromatin architecture in transcription regulation. Finally, we discuss the role of 3D genome alterations in the aetiology of developmental disorders and human diseases.
10.1038/s41580-019-0132-4
Epithelial Properties of the Second Heart Field.
Cortes Claudio,Francou Alexandre,De Bono Christopher,Kelly Robert G
Circulation research
The vertebrate heart tube forms from epithelial progenitor cells in the early embryo and subsequently elongates by progressive addition of second heart field (SHF) progenitor cells from adjacent splanchnic mesoderm. Failure to maximally elongate the heart results in a spectrum of morphological defects affecting the cardiac poles, including outflow tract alignment and atrioventricular septal defects, among the most common congenital birth anomalies. SHF cells constitute an atypical apicobasally polarized epithelium with dynamic basal filopodia, located in the dorsal wall of the pericardial cavity. Recent studies have highlighted the importance of epithelial architecture and cell adhesion in the SHF, particularly for signaling events that control the progenitor cell niche during heart tube elongation. The 22q11.2 deletion syndrome gene regulates progenitor cell status through modulating cell shape and filopodial activity and is required for SHF contributions to both cardiac poles. Noncanonical Wnt signaling and planar cell polarity pathway genes control epithelial polarity in the dorsal pericardial wall, as progenitor cells differentiate in a transition zone at the arterial pole. Defects in these pathways lead to outflow tract shortening. Moreover, new biomechanical models of heart tube elongation have been proposed based on analysis of tissue-wide forces driving epithelial morphogenesis in the SHF, including regional cell intercalation, cell cohesion, and epithelial tension. Regulation of the epithelial properties of SHF cells is thus emerging as a key step during heart tube elongation, adding a new facet to our understanding of the mechanisms underlying both heart morphogenesis and congenital heart defects.
10.1161/CIRCRESAHA.117.310838
Defining Human Pluripotency.
Yilmaz Atilgan,Benvenisty Nissim
Cell stem cell
Human pluripotent stem cells harbor the capacity to differentiate into cells from the three embryonic germ layers, and this ability grants them a central role in modeling human disorders and in the field of regenerative medicine. Here, we review pluripotency in human cells with respect to four different aspects: (1) embryonic development, (2) transcriptomes of pluripotent cell stages, (3) genes and pathways that reprogram somatic cells into pluripotent stem cells, and finally (4) the recent identification of the human pluripotent stem cell essentialome. These four aspects of pluripotency collectively culminate in a broader understanding of what makes a cell pluripotent.
10.1016/j.stem.2019.06.010
Unravelling cellular relationships during development and regeneration using genetic lineage tracing.
Baron Chloé S,van Oudenaarden Alexander
Nature reviews. Molecular cell biology
Tracking the progeny of single cells is necessary for building lineage trees that recapitulate processes such as embryonic development and stem cell differentiation. In classical lineage tracing experiments, cells are fluorescently labelled to allow identification by microscopy of a limited number of cell clones. To track a larger number of clones in complex tissues, fluorescent proteins are now replaced by heritable DNA barcodes that are read using next-generation sequencing. In prospective lineage tracing, unique DNA barcodes are introduced into single cells through genetic manipulation (using, for example, Cre-mediated recombination or CRISPR-Cas9-mediated editing) and tracked over time. Alternatively, in retrospective lineage tracing, naturally occurring somatic mutations can be used as endogenous DNA barcodes. Finally, single-cell mRNA-sequencing datasets that capture different cell states within a developmental or differentiation trajectory can be used to recapitulate lineages. In this Review, we discuss methods for prospective or retrospective lineage tracing and demonstrate how trajectory reconstruction algorithms can be applied to single-cell mRNA-sequencing datasets to infer developmental or differentiation tracks. We discuss how these approaches are used to understand cell fate during embryogenesis, cell differentiation and tissue regeneration.
10.1038/s41580-019-0186-3
Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment.
Xu Qianhua,Xie Wei
Trends in cell biology
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development. The latest studies, including many from genome-wide perspectives, have revealed unusual principles of reprogramming for histone modifications, chromatin accessibility, and 3D chromatin architecture. These advances have shed light on the regulatory network controlling the earliest development and maternal-zygotic transition.
10.1016/j.tcb.2017.10.008
Roles and regulation of histone methylation in animal development.
Jambhekar Ashwini,Dhall Abhinav,Shi Yang
Nature reviews. Molecular cell biology
Histone methylation can occur at various sites in histone proteins, primarily on lysine and arginine residues, and it can be governed by multiple positive and negative regulators, even at a single site, to either activate or repress transcription. It is now apparent that histone methylation is critical for almost all stages of development, and its proper regulation is essential for ensuring the coordinated expression of gene networks that govern pluripotency, body patterning and differentiation along appropriate lineages and organogenesis. Notably, developmental histone methylation is highly dynamic. Early embryonic systems display unique histone methylation patterns, prominently including the presence of bivalent (both gene-activating and gene-repressive) marks at lineage-specific genes that resolve to monovalent marks during differentiation, which ensures that appropriate genes are expressed in each tissue type. Studies of the effects of methylation on embryonic stem cell pluripotency and differentiation have helped to elucidate the developmental roles of histone methylation. It has been revealed that methylation and demethylation of both activating and repressive marks are essential for establishing embryonic and extra-embryonic lineages, for ensuring gene dosage compensation via genomic imprinting and for establishing body patterning via HOX gene regulation. Not surprisingly, aberrant methylation during embryogenesis can lead to defects in body patterning and in the development of specific organs. Human genetic disorders arising from mutations in histone methylation regulators have revealed their important roles in the developing skeletal and nervous systems, and they highlight the overlapping and unique roles of different patterns of methylation in ensuring proper development.
10.1038/s41580-019-0151-1
The diverse roles of DNA methylation in mammalian development and disease.
Greenberg Maxim V C,Bourc'his Deborah
Nature reviews. Molecular cell biology
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
10.1038/s41580-019-0159-6
New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation.
Rossant Janet,Tam Patrick P L
Cell stem cell
Pathways underlying mouse embryonic development have always informed efforts to derive, maintain, and drive differentiation of human pluripotent stem cells. However, direct application of mouse embryology to the human system has not always been successful because of fundamental developmental differences between species. The naive pluripotent state of mouse embryonic stem cells (ESCs), in particular, has been difficult to capture in human ESCs, and appears to be transitory in the human embryo itself. Further studies of human and non-human primate embryo development are needed to untangle the complexities of pluripotency networks across mammalian species.
10.1016/j.stem.2016.12.004
Single-cell transcriptional profiling: a window into embryonic cell-type specification.
Pijuan-Sala Blanca,Guibentif Carolina,Göttgens Berthold
Nature reviews. Molecular cell biology
During mammalian embryonic development, a single fertilized egg cell will proliferate and differentiate into all the cell lineages and cell types that eventually form the adult organism. Cell lineage diversification involves repeated cell fate choices that ultimately occur at the level of the individual cell rather than at the cell-population level. Improvements in single-cell technologies are transforming our understanding of mammalian development, not only by overcoming the limitations presented by the extremely low cell numbers of early embryos but also by enabling the study of cell fate specification in greater detail. In this Review, we first discuss recent advances in single-cell transcriptomics and imaging and provide a brief outline of current bioinformatics methods available to analyse the resulting data. We then discuss how these techniques have contributed to our understanding of pre-implantation and early post-implantation development and of in vitro pluripotency. Finally, we overview the current challenges facing single-cell research and highlight the latest advances and potential future avenues.
10.1038/s41580-018-0002-5
Small RNA regulation of reproductive function.
Hale Benjamin J,Yang Cai-Xia,Ross Jason W
Molecular reproduction and development
Post-transcriptional gene regulation is one mechanism that occurs "above the genome," allowing the cells of an organism to have dramatically different phenotypes and functions. Non-coding ribonucleic acid (ncRNA) molecules regulate transcript and protein abundance above the level of transcription, and appear to play substantial roles in regulation of reproductive tissues. Three primary classes of small ncRNA are microRNA (miRNA), endogenous small interfering RNA (endo-siRNA), and PIWI-interacting RNA (piRNA). These RNA classes have similarities and clear distinctions between their biogenesis and in the interacting protein machinery that facilitate their effects on cellular phenotype. Characterization of the expression and importance of the critical components for the biogenesis of each class in different tissues is continuously contributing a better understanding of each of these RNA classes in different reproductive cell types. Here, we discuss the expression and potential roles of miRNA, endo-siRNA, and piRNA in reproduction from germ-cell development to pregnancy establishment and placental function. Additionally, the potential contribution of RNA binding proteins, long ncRNAs, and the more recently discovered circular RNAs (circRNAs) in relation to small RNA function is discussed.
10.1002/mrd.22272
Long non-coding RNAs as emerging regulators of differentiation, development, and disease.
Dey Bijan K,Mueller Adam C,Dutta Anindya
Transcription
A significant portion of the mammalian genome encodes numerous transcripts that are not translated into proteins, termed long non-coding RNAs. Initial studies identifying long non-coding RNAs inferred these RNA sequences were a consequence of transcriptional noise or promiscuous RNA polymerase II activity. However, the last decade has seen a revolution in the understanding of regulation and function of long non-coding RNAs. Now it has become apparent that long non-coding RNAs play critical roles in a wide variety of biological processes. In this review, we describe the current understanding of long non-coding RNA-mediated regulation of cellular processes: differentiation, development, and disease.
10.4161/21541272.2014.944014
Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging.
Xi Xiaoyu,Zou Qin,Wei Yingying,Chen Yan,Wang Xue,Lv Daojun,Li Peilin,Wen Anxiang,Zhu Li,Tang Guoqing,Ma Jideng,Li Mingzhou,Li Xuewei,Jiang Yanzhi
BioMed research international
The biological function of human ovaries declines along with aging. To identify the underlying molecular changes during ovarian aging, pigs were used as model animals. Genome-wide DNA methylation and transcriptome-wide RNA expression analyses were performed via high-throughput sequencing of ovaries from young pigs (180 days, puberty stage of first ovulation) and old pigs (eight years, reproductive exhaustion stage). The results identified 422 different methylation regions between old and young pigs; furthermore, a total of 2,243 mRNAs, 95 microRNAs, 248 long noncoding RNAs (lncRNAs), and 116 circular RNAs (circRNAs) were differentially expressed during both developmental stages. Gene ontology analysis showed that these genes related to different methylation and expression are involved in the ovarian aging cycle. Specifically, these are involved in cell apoptosis, death effector domain binding, embryonic development, reproduction and fertilization process, ovarian cumulus expansion, and the ovulation cycle. Multigroup cooperative control relationships were also assessed, and competing endogenous RNA (ceRNA) networks were constructed in the ovarian aging cycle. These data will help to clarify ovary age-associated potential molecular changes in DNA methylation and transcriptional patterns over time.
10.1155/2019/8732023
Current status and potential role of circular RNAs in neurological disorders.
Lu Shanshan,Yang Xue,Wang Chudong,Chen Siqi,Lu Shuang,Yan Weitao,Xiong Kun,Liu Fengxia,Yan Jie
Journal of neurochemistry
Given the importance of non-coding RNAs in modulating normal brain functions and their implications in the treatment of neurological disorders, non-coding RNA-based diagnostic and therapeutic strategies have shown great clinical potential. Circular RNAs (circRNAs) have emerged as potentially important players in this field. Recent studies have indicated that circRNAs might play vital roles in Alzheimer's disease, Parkinson's disease, ischemic brain injury, and neurotoxicity. However, the mechanisms of action of circRNAs have not been fully characterized. We aimed to review recent advances in circRNA research in the brain to provide new insights on the roles of circRNAs in neurological disorders.
10.1111/jnc.14724
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular.
Izuogu Osagie G,Alhasan Abd A,Mellough Carla,Collin Joseph,Gallon Richard,Hyslop Jonathon,Mastrorosa Francesco K,Ehrmann Ingrid,Lako Majlinda,Elliott David J,Santibanez-Koref Mauro,Jackson Michael S
BMC genomics
BACKGROUND:Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. RESULTS:A transcriptome-wide increase in circRNA expression, size, and exon count was observed, with circRNA levels reaching a plateau by day 45. Parallel statistical analyses, controlling for sample and locus specific effects, identified 239 circRNAs with expression changes distinct from the transcriptome-wide pattern, but these all also increased in abundance over time. Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes. The most abundant, circRMST:E12-E6, showed a > 100X increase during differentiation accompanied by an isoform switch, and accounts for > 99% of RMST transcripts in many adult tissues. The second most abundant, circFIRRE:E10-E5, accounts for > 98% of FIRRE transcripts in differentiating human ES cells, and is one of 39 FIRRE circRNAs, many of which include multiple unannotated exons. CONCLUSIONS:Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled. They also suggest that RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, are processed as circular lncRNAs with only minor linear species.
10.1186/s12864-018-4660-7
CircFUT10 reduces proliferation and facilitates differentiation of myoblasts by sponging miR-133a.
Li Hui,Yang Jiameng,Wei Xuefeng,Song Chengchuang,Dong Dong,Huang Yongzhen,Lan Xianyong,Plath Martin,Lei Chuzhao,Ma Yun,Qi Xinglei,Bai Yueyu,Chen Hong
Journal of cellular physiology
Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine, and mouse. However, knowledge on circRNAs in bovine muscle development is limited. We downloaded and analyzed the circRNAs sequencing data of bovine skeletal muscle tissue, and further characterized the role of a candidate circRNA (circFUT10) in muscle development. Quantitative real-time PCR (qPCR) and Western blot assays were used to confirm the expression of genes involved in myoblasts differentiation and proliferation. Flow cytometry was performed to assess cell cycle distribution and cell apoptosis. EdU incorporation and CCK-8 assay were performed to demonstrate cell proliferation. We demonstrated that circFUT10 was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. circFUT10 induced bovine primary myoblasts differentiation and increased the expression of MyoD, MyoG, and MyhC in mRNA and protein levels. circFUT10 increased the number of myoblasts in the G0/G1 phase of the cell cycle, and decreased the proportion of cells in the S-phase. circFUT10 inhibited the proliferation of myoblasts and promoted them apoptosis. Via a luciferase screening assay, circFUT10 is observed to sponge to miR-133a with three potential binding sites. Specifically, we show that circFUT10 regulated myoblasts differentiation and cell survival by directly binding to miR-133a and inhibiting miR-133a activity. Modulation of circFUT10 expression in muscle tissue may emerge as a potential target in breeding strategies attempting to control muscle development in cattle.
10.1002/jcp.26230
Circular RNAs and Neuronal Development.
Constantin Lena
Advances in experimental medicine and biology
Circular RNAs (circRNAs) are abundant in the brain and are often expressed in complex spatiotemporal patterns that coincide with distinct developmental transitions. This suggests that circRNAs play a significant role in the central nervous system. This book chapter will review research progress into the function of circRNAs during neuronal development. The major themes to be discussed are the enrichment of circRNAs in the synapse and their possible contributions to synaptopathologies, in addition to the findings that neural circRNAs accumulate with age and appear beneficial for neuronal repair. Although more research is needed, some of the possible functions of circRNAs with in the brain are already beginning to come to light.
10.1007/978-981-13-1426-1_16
Altered expression patterns of circular RNAs between implantation sites and interimplantation sites in early pregnant mice.
Zhang Shuang,Ding Yubin,He Junlin,Zhang Juanjuan,Liu Xueqing,Chen Xuemei,Su Yan,Wang Yingxiong,Gao Rufei
Journal of cellular physiology
Circular RNAs (circRNAs), a class of newly discovered endogenous noncoding RNAs, have been found to play important roles in regulating gene expression and participate in several biological processes. However, their specific roles in embryo implantation remain unclear. This study aims to investigate the roles of circRNAs in embryo implantation. In the current study, we screened the expression profiles of circRNAs between implantation sites and interimplantation sites in the endometrial tissue of early pregnant mice on Day 5 using microarray assay. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) of four dysregulated circRNAs was performed to validate the microarray results. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and circRNA-microRNA (miRNA)-messenger RNA (mRNA) negative correlation network analyses were performed. The microarray results showed 101 upregulated and 75 downregulated circRNAs (fold change [FC] ≥ 1.5 and p value < 0.05) at implantation sites compared with interimplantation sites. Four randomly selected circRNAs were successfully verified by qRT-PCR. The GO and KEGG analyses revealed some meaningful terms. Moreover, based on circRNAs microarray data and the miRNA and mRNA high-throughput data previously published by our groups, differently expressed circRNAs, miRNAs, and mRNAs were performed to conjoint analysis. Then circRNA-miRNA-mRNA negative correlation networks were constructed and 21 downregulated circRNAs, 14 upregulated miRNAs, and 79 downregulated mRNAs were involved in the networks. The findings of this study may provide a novel perspective on circRNAs and lay a foundation for future research into the potential roles of circRNAs in embryo implantation.
10.1002/jcp.27675
An integrated transcriptional analysis of the developing human retina.
Development (Cambridge, England)
The scarcity of embryonic/foetal material as a resource for direct study means that there is still limited understanding of human retina development. Here, we present an integrated transcriptome analysis combined with immunohistochemistry in human eye and retinal samples from 4 to 19 post-conception weeks. This analysis reveals three developmental windows with specific gene expression patterns that informed the sequential emergence of retinal cell types and enabled identification of stage-specific cellular and biological processes, and transcriptional regulators. Each stage is characterised by a specific set of alternatively spliced transcripts that code for proteins involved in the formation of the photoreceptor connecting cilium, pre-mRNA splicing and epigenetic modifiers. Importantly, our data show that the transition from foetal to adult retina is characterised by a large increase in the percentage of mutually exclusive exons that code for proteins involved in photoreceptor maintenance. The circular RNA population is also defined and shown to increase during retinal development. Collectively, these data increase our understanding of human retinal development and the pre-mRNA splicing process, and help to identify new candidate disease genes.
10.1242/dev.169474
Identification of Competing Endogenous RNA Regulatory Networks in Vitamin A Deficiency-Induced Congenital Scoliosis by Transcriptome Sequencing Analysis.
Chen Chong,Tan Haining,Bi Jiaqi,Li Zheng,Rong Tianhua,Lin Youxi,Sun Liang,Li Xingye,Shen Jianxiong
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
BACKGROUND/AIMS:Congenital scoliosis (CS) is a result of anomalous development of vertebrae and is frequently associated with somitogenesis malformation. Although noncoding RNAs (ncRNAs) have been recently determined to be involved in the pathogenesis of CS, the competing endogenous RNA (ceRNA) regulatory networks in CS remain largely unknown. METHODS:Sequencing was conducted to explore the ncRNA expression profiles in rat embryos (gestation day 9) following vitamin A deficiency (VAD) (n = 9 for the vitamin A deficiency-induced congenital scoliosis (VAD-CS) group and n = 4 for the control group). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was conducted to verify the expression levels of selected mRNAs, long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). Bioinformatics analysis was used to discover the possible relationships and functions of the ceRNAs. RESULTS:A total of 749 mRNAs, 56 miRNAs, 685 lncRNAs, and 70 circRNAs were identified to have significantly different expression levels in the two groups. Wnt, PI3K-ATK, FoxO, EGFR, and mTOR were found to be the most significant pathways involved in VAD-CS pathogenesis. The circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks of CS were built, and the gene expression mechanisms regulated by ncRNAs were unveiled via the ceRNA regulatory networks. CONCLUSION:We comprehensively identified ceRNA regulatory networks of embryonic somite development in VAD-CS as well as revealed the contribution of different ncRNA expression profiles. Our data demonstrate the association between mRNAs and ncRNAs in the pathogenic mechanism of CS.
10.1159/000492556
Developmental stage-specific expression of genes for sphingomyelin synthase in rat brain.
Filippenkov Ivan B,Kolomin Timur A,Limborska Svetlana A,Dergunova Lyudmila V
Cell and tissue research
Sphingomyelin synthase genes (Sgms1 and Sgms2) encode the vital enzymes that participate in the processes of membrane transport, cell proliferation and apoptosis. We previously determined the exon-intron structure of Sgms1 and some features of its expression in human and rodent tissues. The circular RNAs (circRNAs) emerging from exons of the 5'-untranslated region (5'-UTR) of Sgms1 were determined. These circRNAs are represented at a high level in the adult brain. Here, we demonstrate that, in contrast to Sgms1, Sgms2 does not contain the multi-exon 5'-UTR but encodes circRNAs, which are composed of the coding region of the gene and are expressed at a low level. We present a study of the expression of sphingomyelin synthase genes in rat brain at embryonic days 7, 9, 13, 17 and 21 and in adult rat brain. In contrast to Sgms1, Sgms2 is expressed at a significantly low level in adult brain. In embryonic rat brain, the mRNA expression of sphingomyelin synthase genes is varied in a developmental stage-specific manner. The level of Sgms1 mRNAs, differing by 5'-UTR-in the formation of which alternative promoters can participate-changes significantly during the process of embryonic development. The expression of circRNAs of Sgms1 was significantly raised during rat embryonic brain development. We assume that the circRNAs are involved in the regulation of sphingomyelin synthase activity in rat brain in different developmental stages.
10.1007/s00441-017-2762-1
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.
Genome biology
Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. This method exhibits robust sensitivity, precision and accuracy. We discover 2891 circRNAs and 913 novel linear transcripts in mouse preimplantation embryos and further analyze the abundance of circRNAs along development, the function of enriched genes, and sequence features of circRNAs. Our work is key to deciphering regulation mechanisms of circRNAs during mammalian early embryonic development.
10.1186/s13059-015-0706-1
Differential expression of circRNAs during rat lung development.
Shen Yan-Qing,Pan Jing-Jing,Sun Zhong-Yi,Chen Xiao-Qing,Zhou Xiao-Guang,Zhou Xiao-Yu,Cheng Rui,Yang Yang
International journal of molecular medicine
At present, thousands of circular RNAs (circRNAs) have been found in cancer and various tissues from different species. However, the expression of circRNAs during rat lung development remains largely unknown. In the present study, circRNA expression profiles were screened in three mixed rat lung tissues at 3 time‑points [embryonic day (E) 19, E21 and post‑natal (P) day 3] during fetal rat development with circRNA high‑throughput sequencing. Preliminary results were verified by reverse transcription‑PCR (RT‑PCR) at 4 time‑points (E16, E19, E21 and P3). A total of 375 circRNAs were differently expressed in E19 vs. E21 (fold change ≥1.5; P<0.05). At the same time, a total of 358 circRNAs were differently expressed in E21 vs. P3 (fold change ≥1.5; P<0.05). A total of 3 circRNAs (rno_circ:chr7:24777879‑24784993, rno_circ:chr14:14620910‑14624933 and rno_circ:chr3:1988750‑1998592) were characterized by having consistent fold changes (≥1.5) between 3 time‑points (E19, E21 and P3) and were selected for RT‑PCR at 4 time‑points (E16, E19, E21 and P3). Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of parent genes of the differentially expressed circRNAs revealed that these circRNAs may serve important roles in lung development. The present results support that these new found circRNAs participate in lung development. Furthermore, these findings may help to clarify the physiopathological mechanism of normal rat lung development, and may further provide a physiopathological basis of lung developmental diseases.
10.3892/ijmm.2019.4299
Regulation of splicing and circularisation of RNA in epithelial mesenchymal plasticity.
Neumann Daniel P,Goodall Gregory J,Gregory Philip A
Seminars in cell & developmental biology
Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes.
10.1016/j.semcdb.2017.08.008
Maternally Inherited Stable Intronic Sequence RNA Triggers a Self-Reinforcing Feedback Loop during Development.
Tay Mandy Li-Ian,Pek Jun Wei
Current biology : CB
Maternally inherited noncoding RNAs (ncRNAs) can regulate zygotic gene expression across generations [1-4]. Recently, many stable intronic sequence RNAs (sisRNAs), which are byproducts of pre-mRNA splicing, were found to be maternally deposited and persist till zygotic transcription in Xenopus and Drosophila [5-7]. In various organisms, sisRNAs can be in linear or circular conformations, and they have been suggested to regulate host gene expression [5-10]. It is unknown whether maternally deposited sisRNAs can regulate zygotic gene expression in the embryos. Here, we show that a maternally inherited sisRNA (sisR-4) from the deadpan locus is important for embryonic development in Drosophila. Mothers, but not fathers, mutant for sisR-4 produce embryos that fail to hatch. During embryogenesis, sisR-4 promotes transcription of its host gene (deadpan), which is essential for development. Interestingly, sisR-4 functions by activating an enhancer present in the intron where sisR-4 is encoded. We propose that a maternal sisRNA triggers expression of its host gene via a positive feedback loop during embryogenesis.
10.1016/j.cub.2017.02.040
Profiling and bioinformatics analyses of differential circular RNA expression in prostate cancer cells.
Future science OA
AIM:There is little knowledge about the expression profile and function of circular RNAs (circRNAs) in prostate cancer (PCa). METHODS:The expression profiles of circRNAs in RWPE-1, 22RV1 and PC3 cells were explored via high-throughput circRNAs sequencing and validated by real-time qPCR. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses. RESULTS:Altogether 9545 circRNAs were identified and hundreds of differentially expressed circRNAs were recognized. CircRNA-miRNA networks analysis showed that many circRNAs, including circSLC7A6, circGUCY1A2 and circZFP57 could cross-talk with tumor-related miRNAs such as miR-21, miR-143 and miR-200 family. CONCLUSION:The results of our bioinformatics analyses suggested that circRNAs should play critical roles in the development and progression of PCa.
10.4155/fsoa-2018-0046
TGF-β- and lipopolysaccharide-induced upregulation of circular RNA PWWP2A promotes hepatic fibrosis via sponging miR-203 and miR-223.
Liu Wentao,Feng Ruo,Li Xingxing,Li Dingyang,Zhai Wenlong
Aging
Both transforming growth factor-beta (TGF-β) and lipopolysaccharide (LPS) can activate hepatic stellate cells (HSCs), thus increasing expressions of alpha smooth muscle actin (α-SMA) and type I collagen alpha 1 (Col1α1) and promoting liver fibrosis. However, whether TGF-β and LPS have a common downstream reactor remains unclear. Recently, a strong relationship of circular RNAs (circRNAs) and fibrogenesis has been elucidated. In this study, we compared the expressions of several circRNAs in TGF-β- and LPS-activated HSCs, and found that circ-PWWP2A was upregulated in both TGF-β- and LPS-activated HSCs and in mouse fibrotic liver tissues. Meanwhile, circ-PWWP2A was positively correlated with HSC activation and proliferation. Two microRNAs, miR-203 and miR-223, were identified to be the downstream targets of circ-PWWP2A using luciferase reporter assay and pull-down interaction assay. Circ-PWWP2A was suggested to promote HSC activation and proliferation via sponging miR-203 and miR-223, and subsequently increasing Fstl1 and TLR4, respectively. Furthermore, downregulating circ-PWWP2A was indicated to alleviate hepatic fibrosis in vivo. In conclusion, our findings indicated that circ-PWWP2A is the common downstream reactor of TGF-β and LPS in HSC activation, and that circ-PWWP2A plays a critical role in hepatic fibrogenesis via sponging miR-203 and miR-223.
10.18632/aging.102405
Circular RNA circPTK2 regulates oxygen-glucose deprivation-activated microglia-induced hippocampal neuronal apoptosis via miR-29b-SOCS-1-JAK2/STAT3-IL-1β signaling.
Wang Huilin,Li Zheng,Gao Jingyan,Liao Qingwu
International journal of biological macromolecules
Oxygen-glucose deprivation (OGD)-activated microglia contribute to neuronal apoptosis via releasing pro-inflammatory cytokines, and some miRNAs have been reported to be involved in this process. Circular RNAs (circRNAs) have been reported to function as miRNA sponges, but it remains unknown whether and how circRNAs contribute to OGD-activated microglia-induced neuronal apoptosis. Here, we investigated the function and relationship of miR-29b and circPTK2 in OGD-activated microglia-induced neuronal apoptosis. We found upregulation of TNF-α and IL-1β, and downregulation of miR-29b in OGD-activated microglia. miR-29b inhibited OGD-activated microglia-induced neuronal apoptosis. Meanwhile, miR-29b promoted SOCS-1 expression, and suppressed JAK2/STAT3 signaling. In addition, inhibition of JAK2/STAT3 signaling downregulated IL-1β expression, while upregulation of miR-29b or SOCS-1 also inhibited IL-1β production. IL-1β was confirmed to be an apoptosis inducer of hippocampal neurons. Moreover, either SOCS-1 upregulation or blockade of JAK2/STAT3 signaling suppressed OGD-activated microglia-induced neuronal apoptosis. These data suggest that miR-29b inhibits OGD-activated microglia-induced neuronal apoptosis via inducing SOCS-1 expression, blocking JNK2/STAT3 signaling, and inhibiting IL-1β production. circPTK2 was confirmed to inhibit miR-29b expression in OGD model by directly binding to miR-29b. Function assay showed that circPTK2 regulated microglia-induced neuronal apoptosis via sponging miR-29b. Collectively, these findings suggest that circPTK2 regulates OGD-activated microglia-induced neuronal apoptosis via miR-29b-SOCS-1-JAK2/STAT3-IL-1β signaling.
10.1016/j.ijbiomac.2019.02.041
Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells.
Li Xiaoyong,Tian Geng G,Zhao Yongqiang,Wu Ji
Scientific data
Germline stem cells are germ cells at an early developmental stage, so their development is key to ensuring human reproduction. There is increasing evidence that long noncoding RNA (lncRNA) and circular RNA (circRNA) play important roles in the development of germ cells. This data descriptor provides unique lncRNA and circRNA transcriptomic information for mouse germline stem cells. Using the Illumina HiSeqx 2000 system, a total of 511,836,732 raw reads were generated. High-quality transcripts, lncRNAs, and circRNAs were identificated and quantified using the reads, and more precise annotations of lncRNAs (especially 9357 novel lncRNAs) and circRNAs were performed in the germline stem cells. We then analyzed the transcript structures, genetic variants, and the interaction between circRNA and microRNA to provide the basis for subsequent functional experiments. This comprehensive dataset will help advance data sharing and deepen our understanding of mouse germline stem cells, providing a theoretical foundation for research on germ cell development and human reproduction, among others.
10.1038/s41597-019-0014-9
Biological functions of circular RNAs and their roles in occurrence of reproduction and gynecological diseases.
Liu Kang-Sheng,Pan Feng,Mao Xiao-Dong,Liu Chao,Chen Ya-Jun
American journal of translational research
Circular RNAs (circRNAs) are a large class of non coding endogenous RNAs in eukaryotic that are formed through 3'-5' ligation of a single RNA molecule. According to the different sources of the sequences, circRNA can be divided into three types: exon circRNA (ecRNA), intron circRNA (ciRNA), and exon-intron circRNA. Accumulating studies have shown that circRNAs are abundant, diverse, stable, and cell or tissue specific expression, etc. CircRNA plays a regulating role in gene expression, and an essential role in the process of biological development, such as miRNA sponges, endogenous RNAs and biomarkers, as well as critical role in the diagnosis of diseases. Studies have verified the interplay between circRNAs and the development of embryos, sperms, ovarian epithelial tumors, endometrial cancer and preeclampsia, suggesting the potential of circRNAs to become biomarkers or therapeutical targets for human diseases. In this paper, we reviewed the researches on circRNAs' characteristics, databases of circRNA, high-throughput sequencing of circRNA, and effect on reproductive and gynecological diseases.
CircRNA-9119 regulates the expression of prostaglandin-endoperoxide synthase 2 (PTGS2) by sponging miR-26a in the endometrial epithelial cells of dairy goat.
Zhang Lei,Liu Xiaorui,Che Sicheng,Cui Jiuzeng,Liu Yuexia,An Xiaopeng,Cao Binyun,Song Yuxuan
Reproduction, fertility, and development
Circular RNAs (circRNAs) have been found to play important functional roles in epigenetic regulation under certain physiological and pathological conditions. However, knowledge of circRNAs during the development of receptive endometrium (RE) from pre-RE is limited. In the RE of dairy goats, higher circRNA-9119 levels, with lower miR-26a and higher prostaglandin-endoperoxide synthase 2 (PTGS2) levels, were detected. Further study showed that circRNA-9119 decreased levels of miR-26a by acting as a microRNA sponge, and that miR-26a downregulated the expression of PTGS2 via the predicted target site in endometrial epithelial cells (EECs) of dairy goats in vitro. In this way, circRNA-9119 functioned as a competing endogenous RNAs (ceRNA) that sequestered miR-26a, thereby protecting PTGS2 transcripts from miR-26a-mediated suppression in dairy goat EECs in vitro. Furthermore, PTGS2 participated in the regulation of some protein markers for endometrial receptivity in dairy goat EECs in vitro. Thus, a circRNA-9119-miR-26a-PTGS2 pathway in the endometrium was identified, and modulation of circRNA-9119-miR-26a-PTGS2 expression in EECs may emerge as a potential target to regulate the development of RE.
10.1071/RD18074
Whole transcriptome sequencing reveals that non-coding RNAs are related to embryo morphogenesis and development in rabbits.
Kuang Liangde,Lei Min,Li Congyan,Guo Zhiqiang,Ren Yongjun,Zhang Xiangyu,Zheng Jie,Zhang Cuixia,Yang Chao,Mei Xiuli,Tang Li,Ji Yang,Deng Xiaodong,Yang Rui,Xie Xiaohong
Genomics
The roles of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in embryonic development remain unclear. We performed a comprehensive analysis of lncRNA and circRNA profiles in rabbit embryos at different stages by whole transcriptome sequencing. We identified 719 lncRNAs and 744 circRNAs that were differentially expressed between stages S1, S2 and S3. A total of 241 differentially expressed lncRNAs and 166 differentially expressed circRNAs were significantly involved in embryonic morphogenesis and development. An RNA network was established and of the embryonic development-associated RNAs, the lncRNAs TCONS_00009253 and TCONS_00010436 were persistently downregulated, while circRNA_07129, circRNA_15209, and circRNA_12526 were persistently upregulated, and their co-expressed mRNAs TBX1, WNT3 and FGFR2 were persistently downregulated during embryonic development. These candidate RNAs were mainly involved in the Wnt, PI3K-Akt, and calcium signaling pathways. This study reports candidate lncRNAs and circRNAs that may be indispensable for the morphogenesis and development of rabbit embryos.
10.1016/j.ygeno.2019.12.016
The circular RNA ciRS-7 promotes APP and BACE1 degradation in an NF-κB-dependent manner.
Shi Zhemin,Chen Ting,Yao Qingbin,Zheng Lina,Zhang Zhen,Wang Jingzhao,Hu Zhimei,Cui Hongmei,Han Yawei,Han Xiaohui,Zhang Kun,Hong Wei
The FEBS journal
The aberrant accumulation of β-amyloid peptide (Aβ) in the brain is a key feature of Alzheimer's disease (AD), and enhanced cleavage of β-amyloid precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) has a major causative role in AD. Despite their prominence in AD pathogenesis, the regulation of BACE1 and APP is incompletely understood. In this study, we report that the circular RNA circular RNA sponge for miR-7 (ciRS-7) has an important role in regulating BACE1 and APP protein levels. Previous studies have shown that ciRS-7, which is highly expressed in the human brain, is down-regulated in the brain of people with AD but the relevance of this finding was not clear. We have found that ciRS-7 is not involved in the regulation of APP and BACE1 gene expression, but instead reduces the protein levels of APP and BACE1 by promoting their degradation via the proteasome and lysosome. Consequently, overexpression of ciRS-7 reduces the generation of Aβ, indicating a potential neuroprotective role of ciRS-7. Our data also suggest that ciRS-7 modulates APP and BACE1 levels in a nuclear factor-κB (NF-κB)-dependent manner: ciRS-7 expression inhibits translation of NF-κB and induces its cytoplasmic localization, thus derepressing expression of UCHL1, which promotes APP and BACE1 degradation. Additionally, we demonstrated that APP reduces the level of ciRS-7, revealing a mutual regulation of ciRS-7 and APP. Taken together, our data provide a molecular mechanism implicating reduced ciRS-7 expression in AD, suggesting that ciRS-7 may represent a useful target in the development of therapeutic strategies for AD.
10.1111/febs.14045
Differential Expression of CircRNAs in Embryonic Heart Tissue Associated with Ventricular Septal Defect.
Liu Heng,Hu Yin,Zhuang Bin,Yin Jing,Chen Xiao-Hui,Wang Juan,Li Meng-Meng,Xu Jing,Wang Xing-Yun,Yu Zhang-Bin,Han Shu-Ping
International journal of medical sciences
To explore and validate the differential expression of circRNAs in the myocardium of congenital ventricular septal defect (VSD) and to explore a new avenue of research regarding the pathological mechanisms of VSD. We detected circRNAs expression profiles in heart tissues taken from six aborted fetuses with VSD and normal group using circRNA microarray. Some differentially expressed circRNAs were studied by bioinformatics analysis. Finally, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm these results. This study found abundant circRNAs in the myocardium taken from individuals in the normal group and the VSD group. After that, totally 6234 differentially expressed circRNAs between the normal group and the VSD group were confirmed (Fold change ≥ 2.0; ). Then, this research carried out bioinformatics analysis and predicted the potential biological functions of circRNAs. Finally, the over-expression of and under-expression of were further validated by qRT-PCR. There is a significant difference in expression of the circRNA in cardiac tissue from VSD group compared to the normal group. Combined with the microarray results and previous researches, circRNAs may contribute to the occurrence of VSD by acting as miRNA sponges or by binding proteins, these possible roles for circRNAs in VSD require elucidation in additional studies.
10.7150/ijms.21660
Circular RNA hsa_circ_0000567 can be used as a promising diagnostic biomarker for human colorectal cancer.
Wang Jianjun,Li Xiaomin,Lu Linming,He Lei,Hu Haoran,Xu Zengxiang
Journal of clinical laboratory analysis
BACKGROUND:Recent studies have revealed that circular RNAs are involved in the biological process of some kinds of human cancers. However, little is known about their diagnostic values and functions in colorectal cancer (CRC). METHODS:The expression levels of hsa_circ_0000567 in 102 paired CRC tissues and adjacent noncancerous tissues, 5 CRC cell lines, and a normal colorectal epithelial cell line were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The correlations between hsa_circ_0000567 expression levels and the clinicopathological factors of patients with CRC were analyzed. Furthermore, the loss-of-function assay was performed to investigate the functions of hsa_circ_0000567 in vitro. Finally, a receiver operating characteristic (ROC) curve was established to evaluate the diagnostic value of hsa_circ_0000567. RESULTS:Hsa_circ_0000567 expression was significantly downregulated in CRC tissues and CRC cell lines. In addition, the decreased hsa_circ_0000567 expression in CRC was negatively correlated with tumor size (P = .011), lymph metastasis (P = .003), distal metastasis (P < .0001), and tumor-node-metastasis (TNM) stage (P = .003) in CRC. Moreover, knockdown of hsa_circ_0000567 promoted CRC cells proliferation and migration in vitro. Importantly, the area under the ROC curve (AUC) was 0.8653, which indicates hsa_circ_0000567 can serve as a diagnostic biomarker. CONCLUSION:Hsa_circ_0000567 may be a novel suppressor and a potential diagnosis biomarker in CRC.
10.1002/jcla.22379
Circular RNA ANKRD36 attends to lipopolysaccharide-aroused MRC-5 cell injury via regulating microRNA-31-3p.
BioFactors (Oxford, England)
BACKGROUND:Some circular RNAs (circRNAs) are reported to attend to the pathogenesis of pneumonia. This study tested the impact of circRNA ankyrin repeat domain 36 (circANKRD36) on human embryonic lung fibroblast MRC-5 cell injury irritated by lipopolysaccharide (LPS). METHODS:After LPS irritation, viability, apoptosis, ROS, protein, and cytokines, along with circANKRD36 were tested by CCK-8, Annexin V-FITC, DCFH-DA, and ELISA or Western blot. si-circANKRD36 and microRNA-31-3p/5p (miR-31-3p/5p) inhibitor were applied to silence circANKRD36 and miR-31-3p/5p. miR-31-3p/5p mimic was utilized to upregulate miR-31-3p/5p. RT-qPCR was used to detect miRNAs. The relationship between miRNAs and MyD88 or IL-34 was analyzed by luciferase activity reporter assay. RESULTS:LPS aroused a decrease in viability, increases in apoptosis, ROS, and IL-6, IL-8, and TNF-α, along with circANKRD36, and activation of NF-κB pathway. Silencing circANKRD36 weakened the above-mentioned influences of LPS. Moreover, silencing circANKRD36 hoisted miR-31-3p expression. Silencing miR-31-3p mitigated the impacts of circANKRD36 silence on LPS-irritated MRC-5 cells. Besides, MyD88 was a downstream target of miR-31-3p, and 3'UTR of IL-34 mRNA was targeted by miR-31-5p. LPS induced the accumulation of MyD88. Silencing MyD88 was constructive to maintain cell viability, retard apoptosis and inhibit adverse oxidation and inflammation. CONCLUSION:This research verified that silencing circANKRD36 could weaken LPS-irritated MRC-5 cell injury via regulating miR-31/MyD88-mediated repression of NF-κB pathway.
10.1002/biof.1592
Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs.
Robic Annie,Faraut Thomas,Djebali Sarah,Weikard Rosemarie,Feve Katia,Maman Sarah,Kuehn Christa
RNA biology
To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 () as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone.
10.1080/15476286.2019.1621621
Profiles analysis reveals circular RNAs involving zebrafish physiological development.
Journal of cellular physiology
Recent studies have found that known functions of circular RNAs (circRNAs) include sequestration of microRNAs (miRNAs) or proteins, modulation of transcription and interference with splicing, and even translation to produce polypeptides. The zebrafish model is also demonstrably similar to humans in many studies. To explore the changes in circRNAs during embryonic development and to further research the mechanism of action of circRNAs in development-related diseases, Zebrafish embryos at the blastula period, gastrula period, segmentation period, throat stage, and incubation period were collected. Illumina deep-sequencing technology and CircRNA Identifier (CIRI) algorithm were used to detect circRNAs. In total, we identified 1,028 circRNAs (junction reads ≥5 and p < 0.05). Considering that the function of circRNAs is related to host genes, a bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways, cardiovascular system development, retinal ganglion cell axon guidance, and so on. Moreover, circRNAs can participate in biological regulation through the function of miRNA sponges. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR-19b, miR-124, and so on. Some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points, suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in a zebrafish model.
10.1002/jcp.28250
Circular RNAs: biogenesis, expression and their potential roles in reproduction.
Journal of ovarian research
Unlike other non-coding RNAs (ncRNAs), circular RNA (circRNA) is generally presented as a covalently linked circle lacking both a 5' cap and a 3' tail. circRNAs were thought to be spliced intermediates, byproducts, or products of abnormal RNA splicing events. However, the high-throughput sequencing technology coupled with bioinformatics has recently uncovered thousands of endogenous circRNAs in cells of many different species. These circRNAs show various features, such as abundant expression, evolutionary conservation, cell- or tissue-specific expression, and a higher resistance to degradation caused by exonuclease or ribonuclease (RNase), suggesting their potentially biological significance. However, the function of these circRNAs, their mechanism of action, and the regulation of their biogenesis and degradation remains largely unclear. The current research and findings of circRNA in the context of reproduction will be reviewed. Additionally, the perspectives of circRNAs in the field will be discussed.
10.1186/s13048-018-0381-4
Circular RNA circITGA7 inhibits colorectal cancer growth and metastasis by modulating the Ras pathway and upregulating transcription of its host gene ITGA7.
Li Xiaomin,Wang Jianjun,Zhang Chao,Lin Chun,Zhang Jianming,Zhang Wei,Zhang Wenjuan,Lu Yanxia,Zheng Lin,Li Xuenong
The Journal of pathology
Circular RNAs (circRNAs) are significantly dysregulated in various cancer types. However, the roles and mechanisms of circRNAs in cancer remain largely unknown. In this study, we demonstrated that a novel circRNA (circITGA7) and its linear host gene ITGA7 are both significantly downregulated in colorectal cancer (CRC) tissues and cell lines. These decreased expression levels correlated with CRC progression. Functional assays demonstrated that ectopic circITGA7 expression suppressed the growth and metastasis of CRC cells in vitro and in vivo. Knockdown of circITGA7 or ITGA7 promoted the proliferation and migration of CRC cells in vitro, and enhanced CRC growth in vivo. Mechanistically, by using RNA-sequencing and KEGG enrichment analysis, we found that circITGA7 is a negative regulator of the Ras signalling pathway, and that ITGA7 is associated with cytokine-related signalling pathways. In addition, circITGA7 binds to miR-370-3p to antagonise its suppression of neurofibromin 1, which is a well-known negative regulator of the Ras pathway. Finally, circITGA7 upregulates the transcription of ITGA7 by suppressing RREB1 via the Ras pathway. In conclusion, our findings indicate a suppressor role of circITGA7 and ITGA7 in CRC, and reveal that circITGA7 inhibits the proliferation and metastasis of CRC cells by suppressing the Ras signalling pathway and promoting the transcription of ITGA7, suggesting that circITGA7 is a potential target for CRC treatment. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
10.1002/path.5125
The roles of circular RNAs in human development and diseases.
Lee Eric Chun Shen,Elhassan Safa Abdelgadir Mohamed,Lim Grace Pei Ling,Kok Weng Hong,Tan Sze Wei,Leong Ee Neng,Tan Sean Hong,Chan Elaine Wan Ling,Bhattamisra Subrat Kumar,Rajendran Ramkumar,Candasamy Mayuren
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
For many years, circular ribonucleic acids (circRNAs) have been counted as aberrant splicing by-products. Advanced bioinformatics analysis and deep sequencing techniques have allowed researchers to discover more interesting facts about circRNAs. Intriguing evidence has shed light on the functions of circRNAs in many tissues. Furthermore, emerging reports showed that circRNAs are found abundantly in saliva and blood samples, suggesting that circRNAs are potential clinical biomarkers for human embryonic development, diseases progression and prognosis, in addition to its role in organogenesis and pathogenesis. The implementation of circRNAs in human developmental stages and diseases would be a tremendous discovery in the science and medical field. Therefore, circRNAs have been studied for its biological function as well as its implication in various human diseases. The aim of this review is to highlight the importance of circRNAs in cardiac, respiratory, nervous, endocrine and digestive systems. In addition, the role and impact of circRNAs in, cardiogenesis, neurogenesis and cancer have been discussed.
10.1016/j.biopha.2018.12.052
Tracing the expression of circular RNAs in human pre-implantation embryos.
Genome biology
BACKGROUND:PolyA- RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA- RNA, has not been characterized during human pre-implantation development. RESULTS:We systematically analyze polyA+ messenger RNAs (mRNAs) and polyA- RNAs in individual human oocytes and pre-implantation embryos using SUPeR-seq. We de novo identify 10,032 circRNAs from 2974 hosting genes. Most of these circRNAs are developmentally stage-specific and dynamically regulated. Many of them are maternally expressed, implying their potentially important regulatory functions in oogenesis and the formation of totipotent zygotes. Comparison between human and mouse embryos reveals both high conservation and clear distinction between these two species. Human pre-implantation embryos generate more types of circRNA compared with mouse embryos and this is associated with a striking increase of the length of the circRNA flanking introns in humans. We also perform RNA de novo assembly and identify novel transcript units, many of which are potentially novel long non-coding RNAs. CONCLUSIONS:This study reports the first analysis of the whole transcriptome comprising both polyA+ mRNAs and polyA- RNAs including circRNAs during human pre-implantation development. It provides an invaluable resource for analyzing the unique function and complex regulatory mechanisms of circRNAs during this process.
10.1186/s13059-016-0991-3
Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development.
Szabo Linda,Morey Robert,Palpant Nathan J,Wang Peter L,Afari Nastaran,Jiang Chuan,Parast Mana M,Murry Charles E,Laurent Louise C,Salzman Julia
Genome biology
BACKGROUND:The pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover, discovering biological contexts where circular RNAs are regulated will shed light on potential functional roles they may play. RESULTS:We present a new algorithm that increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries, including intergenic regions of the genome, with high statistical confidence. Unlike approaches that rely on read count and exon homology to determine confidence in prediction of circular RNA expression, our algorithm uses a statistical approach. Using our algorithm, we unveiled striking induction of general and tissue-specific circular RNAs, including in the heart and lung, during human fetal development. We discover regions of the human fetal brain, such as the frontal cortex, with marked enrichment for genes where circular RNA isoforms are dominant. CONCLUSIONS:The vast majority of circular RNA production occurs at major spliceosome splice sites; however, we find the first examples of developmentally induced circular RNAs processed by the minor spliceosome, and an enriched propensity of minor spliceosome donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, these results suggest a potentially significant role for circular RNA in human development.
10.1186/s13059-015-0690-5
Circular RNA profile in liver tissue of EpCAM knockout mice.
Yang Yanhong,Liu Shaomin,Lei Zili,Chen Guibin,Huang Li,Yang Fei,Lei Yuting,Liu Yanyan,Yang Lanxiang,Liu Wanwan,Lai Liangxue,Guo Jiao
International journal of molecular medicine
Epithelial cell adhesion molecule (EpCAM) is highly expressed during liver development and carcinogenesis, However, its functions and underlying mechanisms remain unclear. Clustered regularly interspaced short palindromic repeats (CRISPRs)/CRISPR‑associated protein 9 (Cas9) technology was used in the current study to establish EpCAM‑/‑ mice. The expression of EpCAM in the livers of the mice at embryonic day (E)18.5 and post‑natal day (P)0 was detected by immunofluorescence staining. The expression of genes associated with the development and glycogen metabolism was also assessed by reverse transcription‑quantitative PCR. Additionally, the liver tissue of the EpCAM‑/‑ and wild‑type mice was used for non‑coding RNA sequencing. The results of RNA sequencing revealed 11 up‑regulated and 12 downregulated circular RNAs (circRNAs). Kyoto Encyclopedia of Genes and Genomes analysis for resource genes determined that the top altered pathways included cell junctions, cell cycle, immune signaling and metabolism. This analysis was also utilized to predict the target association of the circRNA‑microRNA‑mRNA network. The comprehensive liver tissue circRNA expression profiles produced in the present study may help to elucidate the functions and mechanisms of EpCAM during liver development.
10.3892/ijmm.2019.4270
Foxo3 circular RNA promotes cardiac senescence by modulating multiple factors associated with stress and senescence responses.
Du William W,Yang Weining,Chen Yu,Wu Zhong-Kai,Foster Francis Stuart,Yang Zhenguo,Li Xiangmin,Yang Burton B
European heart journal
AIMS:Circular RNAs are a subclass of non-coding RNAs detected within mammalian cells. This study was designed to test the roles of a circular RNA circ-Foxo3 in senescence using in vitro and in vivo approaches. METHODS AND RESULTS:Using the approaches of molecular and cellular biology, we show that a circular RNA generated from a member of the forkhead family of transcription factors, Foxo3, namely circ-Foxo3, was highly expressed in heart samples of aged patients and mice, which was correlated with markers of cellular senescence. Doxorubicin-induced cardiomyopathy was aggravated by ectopic expression of circ-Foxo3 but was relieved by silencing endogenous circ-Foxo3. We also found that silencing circ-Foxo3 inhibited senescence of mouse embryonic fibroblasts and that ectopic expression of circ-Foxo3 induced senescence. We found that circ-Foxo3 was mainly distributed in the cytoplasm, where it interacted with the anti-senescent protein ID-1 and the transcription factor E2F1, as well as the anti-stress proteins FAK and HIF1α. CONCLUSION:We conclude that ID-1, E2F1, FAK, and HIF1α interact with circ-Foxo3 and are retained in the cytoplasm and could no longer exert their anti-senescent and anti-stress roles, resulting in increased cellular senescence.
10.1093/eurheartj/ehw001
MyoD-induced circular RNA CDR1as promotes myogenic differentiation of skeletal muscle satellite cells.
Li Li,Chen Yuan,Nie Lu,Ding Xue,Zhang Xiao,Zhao Wei,Xu Xiaoli,Kyei Bismark,Dai Dinghui,Zhan Siyuan,Guo Jiazhong,Zhong Tao,Wang Linjie,Zhang Hongping
Biochimica et biophysica acta. Gene regulatory mechanisms
Many protein coding and non-coding genes interplay in governing skeletal muscle formation. Nevertheless, comparing with the linear transcripts, functions of covalently closed circular RNAs (circRNAs), the new frontier of regulatory non-coding RNA (ncRNAs) molecules, remain largely unknown. Here, we identify CDR1as (antisense to the cerebellar degeneration-related protein 1 transcript, also termed as ciRS-7), a well-known cancer and neuron circRNA, plays a significant role in virtually controlling muscle differentiation. CDR1as is highly expressed in muscles of the mid-embryonic goat foetus, and activated at the initiation of myogenic differentiation in vitro. MyoD (myogenic differentiation protein 1), a driven transcription factor for myogenesis, promotes CDR1as by binding on its 5' flank region (-646 to -634 bp, neighbouring the predicted transcription start site at -580 bp). Overexpression or knockdown of CDR1as dramatically induces or impedes muscle differentiation program, respectively. By competitively binding to miR-7 (microRNA 7), CDR1as relieves the downregulation of IGF1R (insulin like growth factor 1 receptor) caused by miR-7 and consequently activates muscle differentiation. These results unveil that CDR1as plays critical roles in myogenic differentiation, which extends the versatile functions of CDR1as in mammal development and disease.
10.1016/j.bbagrm.2019.07.001
Genome-Wide Analysis of Circular RNAs Mediated ceRNA Regulation in Porcine Embryonic Muscle Development.
Hong Linjun,Gu Ting,He Yanjuan,Zhou Chen,Hu Qun,Wang Xingwang,Zheng Enqin,Huang Sixiu,Xu Zheng,Yang Jie,Yang Huaqiang,Li Zicong,Liu Dewu,Cai Gengyuan,Wu Zhenfang
Frontiers in cell and developmental biology
Many circular RNAs (circRNAs) have been discovered in various tissues and cell types in pig. However, the temporal expression pattern of circRNAs during porcine embryonic muscle development remains unclear. Here, we present a panorama view of circRNA expression in embryonic muscle development at 33-, 65-, and 90-days post-coitus (dpc) from Duroc pigs. An unbiased analysis reveals that more than 5,000 circRNAs specifically express in embryonic muscle development. The amount and complexity of circRNA expression is most pronounced in skeletal muscle at day 33 of gestation. Our circRNAs annotation analyses show that "hot-spot" genes produce multiple circRNA isoforms and RNA binding protein (RBPs) may regulate the biogenesis of circRNAs. Furthermore, we observed that host genes of differentially expressed circRNA across porcine muscle development are enriched in skeletal muscle function. A competing endogenous RNA (ceRNA) network analysis of circRNAs reveals that circRNAs regulate muscle gene expression by functioning as miRNA sponges. Finally, our experimental validation demonstrated that circTUT7 regulate the expression of HMG20B in a ceRNA mechanism. Our analyses show that circRNAs are dynamically expressed and interacting with muscle genes through ceRNA manner, suggesting their critical functions in embryonic skeletal muscle development.
10.3389/fcell.2019.00289
Circular RNAs are abundant and dynamically expressed during embryonic muscle development in chickens.
Ouyang Hongjia,Chen Xiaolan,Wang Zhijun,Yu Jiao,Jia Xinzheng,Li Zhenhui,Luo Wei,Abdalla Bahareldin Ali,Jebessa Endashaw,Nie Qinghua,Zhang Xiquan
DNA research : an international journal for rapid publication of reports on genes and genomes
The growth and development of skeletal muscle is regulated by proteins as well as non-coding RNAs. Circular RNAs (circRNAs) are universally expressed in various tissues and cell types, and regulate gene expression in eukaryotes. To identify the circRNAs during chicken embryonic skeletal muscle development, leg muscles of female Xinghua (XH) chicken at three developmental time points 11 embryo age (E11), 16 embryo age (E16) and 1 day post hatch (P1) were performed RNA sequencing. We identified 13,377 circRNAs with 3,036 abundantly expressed and most were derived from coding exons. A total of 462 differentially expressed circRNAs were identified (fold change > 2; q-value < 0.05). Parental genes of differentially expressed circRNAs were related to muscle biological processes. There were 946 exonic circRNAs have been found that harbored one or more miRNA-binding site for 150 known miRNAs. We validated that circRBFOX2s promoted cell proliferation through interacted with miR-206. These data collectively indicate that circRNAs are abundant and dynamically expressed during embryonic muscle development and could play key roles through sequestering miRNAs as well as other functions.
10.1093/dnares/dsx039
Circular RNA Promotes Myoblast Proliferation and Differentiation by Sponging miR-203 in Chicken.
Ouyang Hongjia,Chen Xiaolan,Li Weimin,Li Zhenhui,Nie Qinghua,Zhang Xiquan
Frontiers in genetics
Circular RNAs (circRNAs), expressed abundantly and universally in various eukaryotes, are involved in growth and development of animals. Our previous study on circRNA sequencing revealed that , an exonic circular, expressed differentially among skeletal muscle at 11 embryo age (E11), 16 embryo age (E16), and 1 day post-hatch (P1). In this study, we aim to investigate the effect of on the development of skeletal muscle. We detected the expression level of in embryonic leg muscle during E10 to P1. As a result, we found that had a high expression level during late embryonic development of skeletal muscle. Through dual-luciferase assay, RNA immunoprecipitation and biotin-coupled miRNA pull down, we found chicken could functions as miR-203 sponges and upregulated the mRNA level of and . In chicken, could promote the proliferation and differentiation of myoblast, and antagonize the functions of miR-203. Altogether our data suggest that promotes the embryonic skeletal muscle development by sequestering miR-203 in chicken.
10.3389/fgene.2018.00172
Dynamic Organization of lncRNA and Circular RNA Regulators Collectively Controlled Cardiac Differentiation in Humans.
EBioMedicine
Advances in developmental cardiology have increased our understanding of the early aspects of heart differentiation. However, understanding noncoding RNA (ncRNA) transcription and regulation during this process remains elusive. Here, we constructed transcriptomes for both long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in four important developmental stages ranging from early embryonic to cardiomyocyte based on high-throughput sequencing datasets, which indicate the high stage-specific expression patterns of two ncRNA types. Additionally, higher similarities of samples within each stage were found, highlighting the divergence of samples collected from distinct cardiac developmental stages. Next, we developed a method to identify numerous lncRNA and circRNA regulators whose expression was significantly stage-specific and shifted gradually and continuously during heart differentiation. We inferred that these ncRNAs are important for the stages of cardiac differentiation. Moreover, transcriptional regulation analysis revealed that the expression of stage-specific lncRNAs is controlled by known key stage-specific transcription factors (TFs). In addition, circRNAs exhibited dynamic expression patterns independent from their host genes. Functional enrichment analysis revealed that lncRNAs and circRNAs play critical roles in pathways that are activated specifically during heart differentiation. We further identified candidate TF-ncRNA-gene network modules for each differentiation stage, suggesting the dynamic organization of lncRNAs and circRNAs collectively controlled cardiac differentiation, which may cause heart-related diseases when defective. Our study provides a foundation for understanding the dynamic regulation of ncRNA transcriptomes during heart differentiation and identifies the dynamic organization of novel key lncRNAs and circRNAs to collectively control cardiac differentiation.
10.1016/j.ebiom.2017.09.015
Profiling circular RNA in methamphetamine-treated primary cortical neurons identified novel circRNAs related to methamphetamine addiction.
Li Junwei,Shi Qingqing,Wang Qian,Tan Xu,Pang Kunkun,Liu Xiaoyu,Zhu Shaowei,Xi Kaiyan,Zhang Jing,Gao Qing,Hu Yanlai,Sun Jinhao
Neuroscience letters
Methamphetamine (METH) has been a worldwide health threat for years. Recent studies have reported that circular RNA (circRNA) are highly abundant and dynamically expressed in brain. However, connections between circRNA and METH-induced neurotoxicity remains indefinite. In the present study, primary cortical neurons were treated with METH in vitro. We profiled circRNA via high-throughput RNA sequencing and identified 2458 circRNAs. Bioinformatics analysis was performed to predict potential functions of these circRNAs which revealed several relevant pathways including 'morphine addiction' that may contribute to the pathogenesis of neuronal damage by METH. Especially, a METH-addicted mouse model was established with conditional place preference paradigm for validation of screened circRNAs. At last, we established co-expression networks of circRNAs with miRNAs and mRNAs to exhibit potential association among them. In conclusion, we firstly unveiled a role of circRNAs in METH-induced neuronal damage and METH addiction.
10.1016/j.neulet.2019.02.032
Circular RNA circHIPK3 Promotes the Proliferation and Differentiation of Chicken Myoblast Cells by Sponging miR-30a-3p.
Chen Biao,Yu Jiao,Guo Lijin,Byers Mary Shannon,Wang Zhijun,Chen Xiaolan,Xu Haiping,Nie Qinghua
Cells
Circular RNAs and microRNAs widely exist in various species and play crucial roles in multiple biological processes. It is essential to study their roles in myogenesis. In our previous sequencing data, both miR-30a-3p and circular HIPK3 (circHIPK3) RNA, which are produced by the third exon of the gene, were differentially expressed among chicken skeletal muscles at 11 embryo age (E11), 16 embryo age (E16), and 1-day post-hatch (P1). Here, we investigated their potential roles in myogenesis. Proliferation experiment showed that miR-30a-3p could inhibit the proliferation of myoblast. Through dual-luciferase assay and Myosin heavy chain (MYHC) immunofluorescence, we found that miR-30a-3p could inhibit the differentiation of myoblast by binding to Myocyte Enhancer Factor 2 C (), which could promote the differentiation of myoblast. Then, we found that circHIPK3 could act as a sponge of miR-30a-3p and exerted a counteractive effect of miR-30a-3p by promoting the proliferation and differentiation of myoblasts. Taking together, our data suggested that circHIPK3 could promote the chicken embryonic skeletal muscle development by sponging miR-30a-3p.
10.3390/cells8020177
Single-Cell Non-coding RNA in Embryonic Development.
Fu Qiang,Liu Chuan-Jiang,Zhai Zhen-Sheng,Zhang Xu,Qin Tao,Zhang Hong-Wei
Advances in experimental medicine and biology
Non-coding RNAs (ncRNAs) have significant regulatory functions on the regulation of gene expression of various life activities after transcription, even though they do not encode proteins. During the development of embryos, ncRNAs, such as long non-coding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and Piwi-interacting RNAs (piRNAs), have been widely proven as key regulators. The emerging single-cell RNA sequencing technique is powerful for profiling "cell-to-cell" variability at the genomic level. It has been applied to detect the expression of ncRNAs during embryo development. In this chapter, we pay close attention to single-cell ncRNA expression and summarize their roles in embryo development.
10.1007/978-981-13-0502-3_3
Circular RNA profiling reveals an abundant circLMO7 that regulates myoblasts differentiation and survival by sponging miR-378a-3p.
Wei Xuefeng,Li Hui,Yang Jiameng,Hao Dan,Dong Dong,Huang Yongzhen,Lan Xianyong,Plath Martin,Lei Chuzhao,Lin Fengpeng,Bai Yueyu,Chen Hong
Cell death & disease
Circular RNAs (circRNAs) have been identified from various tissues and species, but their regulatory functions during developmental processes are not well understood. We examined circRNA expression profiles of two developmental stages of bovine skeletal muscle (embryonic and adult musculus longissimus) to provide first insights into their potential involvement in bovine myogenesis. We identified 12 981 circRNAs and annotated them to the Bos taurus reference genome, including 530 circular intronic RNAs (ciRNAs). One parental gene could generate multiple circRNA isoforms, with only one or two isoforms being expressed at higher expression levels. Also, several host genes produced different isoforms when comparing development stages. Most circRNA candidates contained two to seven exons, and genomic distances to back-splicing sites were usually less than 50 kb. The length of upstream or downstream flanking introns was usually less than 105 nt (mean≈11 000 nt). Several circRNAs differed in abundance between developmental stages, and real-time quantitative PCR (qPCR) analysis largely confirmed differential expression of the 17 circRNAs included in this analysis. The second part of our study characterized the role of circLMO7-one of the most down-regulated circRNAs when comparing adult to embryonic muscle tissue-in bovine muscle development. Overexpression of circLMO7 inhibited the differentiation of primary bovine myoblasts, and it appears to function as a competing endogenous RNA for miR-378a-3p, whose involvement in bovine muscle development has been characterized beforehand. Congruent with our interpretation, circLMO7 increased the number of myoblasts in the S-phase of the cell cycle and decreased the proportion of cells in the G0/G1 phase. Moreover, it promoted the proliferation of myoblasts and protected them from apoptosis. Our study provides novel insights into the regulatory mechanisms underlying skeletal muscle development and identifies a number of circRNAs whose regulatory potential will need to be explored in the future.
10.1038/cddis.2017.541
Circular RNA expression in human hematopoietic cells is widespread and cell-type specific.
Nucleic acids research
Hematopoietic stem cells differentiate into a broad range of specialized blood cells. This process is tightly regulated and depends on transcription factors, micro-RNAs, and long non-coding RNAs. Recently, also circular RNA (circRNA) were found to regulate cellular processes. Their expression pattern and their identity is however less well defined. Here, we provide the first comprehensive analysis of circRNA expression in human hematopoietic progenitors, and in differentiated lymphoid and myeloid cells. We here show that the expression of circRNA is cell-type specific, and increases upon maturation. CircRNA splicing variants can also be cell-type specific. Furthermore, nucleated hematopoietic cells contain circRNA that have higher expression levels than the corresponding linear RNA. Enucleated blood cells, i.e. platelets and erythrocytes, were suggested to use RNA to maintain their function, respond to environmental factors or to transmit signals to other cells via microvesicles. Here we show that platelets and erythrocytes contain the highest number of circRNA of all hematopoietic cells, and that the type and numbers of circRNA changes during maturation. This cell-type specific expression pattern of circRNA in hematopoietic cells suggests a hithero unappreciated role in differentiation and cellular function.
10.1093/nar/gky721
Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation.
Cao Zubing,Gao Di,Xu Tengteng,Zhang Ling,Tong Xu,Zhang Dandan,Wang Yiqing,Ning Wei,Qi Xin,Ma Yangyang,Ji Kaiyuan,Yu Tong,Li Yunsheng,Zhang Yunhai
Aging
Thousands of circular RNAs (circRNAs) have been recently discovered in cumulus cells and oocytes from several species. However, the expression and function of circRNA during porcine oocyte meiotic maturation have been never examined. Here, we separately identified 7,067 and 637 circRNAs in both cumulus cells and oocytes via deep sequencing and bioinformatic analysis. Further analysis revealed that a faction of circRNAs is differentially expressed (DE) in a developmental stage-specific manner. The host genes of DE circRNAs are markedly enriched to multiple signaling pathways associated with cumulus cell function and oocyte maturation. Additionally, most DE circRNAs harbor several miRNA targets, suggesting that these DE circRNAs potentially act as miRNA sponge. Importantly, we found that maternal knockdown by siRNA microinjection caused a severely impaired chromosome alignment, and significantly inhibited first polar body extrusion and early embryo development. Taken together, these results demonstrate for the first time that circRNAs are abundantly and dynamically expressed in a developmental stage-specific manner in cumulus cells and oocytes, and maternally expressed is essential for porcine oocyte meiotic maturation and early embryo development.
10.18632/aging.102315
Circular RNA differential expression in blood cell populations and exploration of circRNA deregulation in pediatric acute lymphoblastic leukemia.
Gaffo Enrico,Boldrin Elena,Dal Molin Anna,Bresolin Silvia,Bonizzato Annagiulia,Trentin Luca,Frasson Chiara,Debatin Klaus-Michael,Meyer Lueder H,Te Kronnie Geertruij,Bortoluzzi Stefania
Scientific reports
Circular RNAs (circRNAs) are abundantly expressed in the haematopoietic compartment, but knowledge on their diversity among blood cell types is still limited. Nevertheless, emerging data indicate an array of circRNA functions exerted through interactions with other RNAs and proteins, by translation into peptides, and circRNA involvement as regulatory molecules in many biological processes and cancer mechanisms. Interestingly, the role of specific circRNAs in leukemogenesis has been disclosed by a few studies, mostly in acute myeloid leukemia. In this study, circRNA expression in B-cells, T-cells and monocytes of healthy subjects is described, including putative new circRNA genes. Expression comparison considered 6,228 circRNAs and highlighted cell population-specific expression and exon usage patterns. Differential expression has been confirmed by qRT-PCR for circRNAs specific of B-cells (circPAX5, circAFF3, circIL4R, and circSETBP1) or T-cells (circIKZF1, circTNIK, circTXK, and circFBXW7), and for circRNAs from intronic (circBCL2) and intergenic regions that were overexpressed in lymphocytes. Starting from this resource of circRNA expression in mature blood cell populations, targeted examination identified striking and generalized upregulated expression of circPAX5, circPVT1 and circHIPK3 in pediatric B-precursor acute lymphoblastic leukemia, and disclosed circRNAs with variable expression across cytogenetic subtypes.
10.1038/s41598-019-50864-z
Circular RNA profiling identified an abundant circular RNA circTMTC1 that inhibits chicken skeletal muscle satellite cell differentiation by sponging miR-128-3p.
International journal of biological sciences
Myogenesis involves a series of complex cellular and developmental processes regulated by many genes, transcription factors and non-coding RNAs. Recent studies have demonstrated the involvement of circular RNAs (circRNAs) in myogenesis. While previous studies have established a role for some circRNAs, the precise functions and mechanisms of circRNAs in skeletal muscle development are still not completely understood in chicken. To identify potential circRNAs during chicken embryonic skeletal muscle development, rRNA libraries sequencing was performed in breast muscles from 12 broilers and 12 layers at four different embryonic points, embryonic day 10 (E10), E13, E16 and E19. Through circRNA differential expression analysis and target miRNA prediction, the circTMTC1 was predicted to participate in the embryonic muscle formation by sponging miRNA, which were verified in vitro experiments. We identified 228 differentially expressed circRNAs between broilers and layers (fold change >2; p-value < 0.05), and 43 circRNAs were differentially expressed at multiple embryonic days. circTMTC1, a novel circRNA transcribed from the TMTC1 gene, was expressed significantly higher in layers than in broilers at E10, E13 and E16. Furthermore, circTMTC1 knockdown accelerated proliferation and differentiation in chicken skeletal muscle satellite cells (SMSCs), besides, circTMTC1-overexpressing cells showed opposite effects. circTMTC1 functioned as a miR-128-3p sponge at the differentiation stage of SMSCs, and circTMTC1 inhibited the expression of miR-128-3p. Furthermore, miR-128-3p promoted differentiation of chicken SMSCs, and circTMTC1 inhibited the promotion effect of miR-128-3p on chicken SMSC differentiation. Our study revealed that circRNAs are differentially expressed during chicken embryonic development between the two chicken models, and circTMTC1 inhibits chicken SMSC differentiation by sponging miR-128-3p.
10.7150/ijbs.36412
Changes in circular RNA expression patterns during human foetal brain development.
Chen Bei Jun,Huang Suleigh,Janitz Michael
Genomics
Circular RNAs (circRNAs) are a recently identified class of long non-coding RNAs and their expression is regulated in a tissue- and developmental stage-specific manner. Recent studies indicate the potential regulatory role that circRNAs may have, particularly in the brain, where they are most abundant. This study aims to elucidate changes in circRNA patterns during human embryonic brain development. We detected a number of differentially expressed genes that showed distinct expression profiles for circular and linear transcripts despite having originated from the same genes, implicating a dichotomy in the regulation of these two RNA species. Altogether our study showed that circular and linear RNAs have independent expression patterns, and that circular transcriptomes from different developing stages have distinct characteristics in terms of transcript abundance and isoform diversity.
10.1016/j.ygeno.2018.04.015
Identification of circular RNA-associated competing endogenous RNA network in the development of cleft palate.
Shu Xuan,Cheng Liuhanghang,Dong Zejun,Shu Shenyou
Journal of cellular biochemistry
Circular RNAs (circRNAs) serve as competing endogenous RNAs (ceRNAs) and indirectly regulate gene expression through shared microRNAs (miRNAs). However, the regulatory mechanisms of circRNA as ceRNA associated with the fusion of palatal shelves in palatogenesis are yet unclear. This study aimed to explore the potential mechanism underlying the role of circRNA as ceRNA in cleft palate (CP). First, we systematically analyzed RNA-seq and miRNA-seq data after high-throughput sequencing for embryonic palatal shelf tissues from a mouse CP model induced by maternal exposure to all-trans retinoic acid on embryonic gestation day 14.5 (E14.5). Thirty-nine circRNAs, 18 miRNAs, and 936 messenger RNAs (mRNAs) were significantly dysregulated (log [fold change {FC}] > 1; P < 0.05). Thereafter, we constructed a circRNA-associated ceRNA network. Finally, we determined the circRNA_0954-miRNA-881-3p-PRKAR1α ceRNA network as a hub involved in palatogenesis. Gene Ontology analysis revealed that ceRNA-related genes were associated with facial morphogenesis and developmental gene silencing. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that ceRNA-related genes are involved in apoptosis (P < 0.05, fold enrichment >1). Quantitative reverse transcription polymerase chain reaction was performed to verify the results of ceRNA analysis. We found that the circRNA-miRNA-mRNA ceRNA network is involved in palatogenesis. The present results imply that circRNA_0954-miRNA-881-3p-PRKAR1α ceRNA network may cause dysfunctional palatal fusion and might facilitate the development of novel epigenetic biomarkers to treat CP in the future.
10.1002/jcb.28888
Exposure to Ionizing Radiation Triggers Prolonged Changes in Circular RNA Abundance in the Embryonic Mouse Brain and Primary Neurons.
Cells
The exposure of mouse embryos in utero and primary cortical neurons to ionizing radiation results in the P53-dependent activation of a subset of genes that is highly induced during brain development and neuronal maturation, a feature that these genes reportedly share with circular RNAs (circRNAs). Interestingly, some of these genes are predicted to express circular transcripts. In this study, we validated the abundance of the circular transcript variants of four P53 target genes (, , and ). These circular variants were overall more stable than their linear counterparts. They were furthermore highly enriched in the brain and their transcript levels continuously increase during subsequent developmental stages (from embryonic day 12 until adulthood), while no further increase could be observed for linear mRNAs beyond post-natal day 30. Finally, whereas radiation-induced expression of P53 target mRNAs peaks early after exposure, several of the circRNAs showed prolonged induction in irradiated embryonic mouse brain, primary mouse cortical neurons, and mouse blood. Together, our results indicate that the circRNAs from these P53 target genes are induced in response to radiation and they corroborate the findings that circRNAs may represent biomarkers of brain age. We also propose that they may be superior to mRNA as long-term biomarkers for radiation exposure.
10.3390/cells8080778
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development.
Venø Morten T,Hansen Thomas B,Venø Susanne T,Clausen Bettina H,Grebing Manuela,Finsen Bente,Holm Ida E,Kjems Jørgen
Genome biology
BACKGROUND:Recently, thousands of circular RNAs (circRNAs) have been discovered in various tissues and cell types from human, mouse, fruit fly and nematodes. However, expression of circRNAs across mammalian brain development has never been examined. RESULTS:Here we profile the expression of circRNA in five brain tissues at up to six time-points during fetal porcine development, constituting the first report of circRNA in the brain development of a large animal. An unbiased analysis reveals a highly complex regulation pattern of thousands of circular RNAs, with a distinct spatio-temporal expression profile. The amount and complexity of circRNA expression was most pronounced in cortex at day 60 of gestation. At this time-point we find 4634 unique circRNAs expressed from 2195 genes out of a total of 13,854 expressed genes. Approximately 20 % of the porcine splice sites involved in circRNA production are functionally conserved between mouse and human. Furthermore, we observe that "hot-spot" genes produce multiple circRNA isoforms, which are often differentially expressed across porcine brain development. A global comparison of porcine circRNAs reveals that introns flanking circularized exons are longer than average and more frequently contain proximal complementary SINEs, which potentially can facilitate base pairing between the flanking introns. Finally, we report the first use of RNase R treatment in combination with in situ hybridization to show dynamic subcellular localization of circRNA during development. CONCLUSIONS:These data demonstrate that circRNAs are highly abundant and dynamically expressed in a spatio-temporal manner in porcine fetal brain, suggesting important functions during mammalian brain development.
10.1186/s13059-015-0801-3