promoted adipocyte differentiation by regulating gene through mA modification in Hycole rabbits.
Animal biotechnology
N6-methyladenosine (mA), the most abundant internal mRNA modification in eukaryotes, plays a vital role in regulating adipogenesis. However, its underlying mechanism remains largely unknown. Our previous study found that gene has mA modification in both muscle and fat tissue. In this study, we interfered with and genes After we cultured rabbit preadipocytes respectively. Oil red O staining and triglyceride assay were used to detect adipocyte differentiation. RT-qPCR was used to detect gene expression level and MeRIP-qPCR was used to detect the mA modification level of gene. The results showed that promoted the differentiation of adipocytes. At the same time, up regulated the expression of gene and down regulated the mA modification level of gene. Finally, we found that inhibited adipocyte differentiation. Together, we showed that promoted adipocyte differentiation by regulating gene through mA modification.
10.1080/10495398.2022.2105229
Reproductive Performance of Hycole Rabbit Does, Growth of Kits and Milk Chemical Composition during Nine Consecutive Lactations under Extensive Rhythm.
Ludwiczak Agnieszka,Składanowska-Baryza Joanna,Kuczyńska Beata,Sell-Kubiak Ewa,Stanisz Marek
Animals : an open access journal from MDPI
The goal of this study was to analyze the reproductive performance of does, growth of their kits, and chemical composition of their milk over nine consecutive parities in order to indicate the boundary of female reproductive profitability. The novelty of this study results from the combinations of three factors: extensive reproductive rhythm, commercial farming conditions, and a period of nine consecutive parities, showing the actual lifespan of a rabbit doe on commercial farms. The data was collected on 60 Hycole females kept at a commercial rabbit farm. Throughout the study, 32 does were excluded due to different reasons (e.g., excluded by means of selection-43.8% and mortalities-25.0%). The does were first inseminated at 28 weeks of age. Following artificial inseminations were conducted 14-15 days after each parturition. All kits were weaned at the age of 35 days. The following characteristics were analysed: body weight of rabbit does at artificial insemination, milk production per lactation, litter size, litter weight, average kit weight, and milk chemical composition. Rabbit does had a significant decrease in kindling rate between the eighth and the ninth parity (by 10.0 percentage points; = 0.039). The litter size at weaning in the ninth parity was significantly lower to litters weaned at other analysed parities. The amount of milk produced per lactation was affected by the parity order (6.31-6.76 kg; = 0.042). The litter weights on day 21 and 35 were the lowest at ninth parity. The content of total solids (TS), solids-not-fat, and fat was affected by the parity order on both analysed lactation days. The content of TS and fat in rabbit milk was characterized with a decreasing trend over the analysed period, on both lactation days. The results clearly indicate that rabbit does under extensive reproductive cycles characterize with a very good reproductive performance and can be successfully used for reproduction even up to the eighth parity. However, further research is needed if keeping them longer will not be profitable.
10.3390/ani11092608
Gene expression profiling analysis reveals fur development in rex rabbits (Oryctolagus cuniculus).
Zhao BoHao,Chen Yang,Yan XiaoRong,Hao Ye,Zhu Jie,Weng QiaoQing,Wu XinSheng
Genome
Fur is an important economic trait in rabbits. The identification of genes that influence fur development and knowledge regarding the actions of these genes provides useful tools for improving fur quality. However, the mechanism of fur development is unclear. To obtain candidate genes related to fur development, the transcriptomes of tissues from backs and bellies of Chinchilla rex rabbits were compared. Of the genes analyzed, 336 showed altered expression in the two groups (285 upregulated and 51 downregulated, P ≤ 0.05, fold-change ≥2 or ≤0.5). Using GO and KEGG to obtain gene classes that were differentially enriched, we found several genes to be involved in many important biological processes. In addition, we identified several signaling pathways involved in fur development, including the Wnt and MAPK signaling pathways, revealing mechanisms of skin and hair follicle development, and epidermal cell and keratinocytes differentiation. The obtained rabbit transcriptome and differentially expressed gene profiling data provided comprehensive gene expression information for SFRP2, FRZB, CACNG1, SLC25A4, and SLC16A3. To validate the RNA-seq data, the expression levels of eight differentially expressed genes involved in fur development were confirmed by qRT-PCR. The results of rabbit transcriptomic profiling provide a basis for understanding the molecular mechanisms of fur development.
10.1139/gen-2017-0003
Integrated single cell transcriptome sequencing analysis reveals species-specific genes and molecular pathways for pig spermiogenesis.
Reproduction in domestic animals = Zuchthygiene
Mammalian spermatogenesis is a highly complicated and intricately organized process involving spermatogonia propagation (mitosis) and meiotic differentiation into mature sperm cells (spermiogenesis). In pigs, spermatogonia development and the role of somatic cells in spermatogenesis were previously investigated in detail. However, the characterization of key molecules fundamental to pig spermiogenesis remains less explored. Here we compared spermatogenesis between humans and pigs, focusing on spermiogenesis, by integrative testicular single-cell RNA sequencing (scRNA-seq) analysis. Human and pig testicular cells were clustered into 26 different groups, with cell-type-specific markers and signalling pathways. For spermiogenesis, pseudo-time analysis classified the lineage differentiation routes for round, elongated spermatids and spermatozoa. Moreover, markers and molecular pathways specific to each type of spermatids were examined for humans and pigs, respectively. Furthermore, high-dimensional weighted gene co-expression network analysis (hdWGCNA) identified gene modules specific for each type of human and pig spermatids. Hub genes (pig: SNRPD2.1 related to alternative splicing; human: CATSPERZ, Ca[2+] ion channel) potentially involved in spermiogenesis were also revealed. Taken together, our integrative analysis found that human and pig spermiogeneses involve specific genes and molecular pathways and provided resources and insights for further functional investigation on spermatid maturation and male reproductive ability.
10.1111/rda.14493
An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs.
International journal of molecular sciences
Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including , , , , , , , , , , and , with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, , , and , which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.
10.3390/ijms241914812
RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics.
Methods in molecular biology (Clifton, N.J.)
The principal transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) has several advantages over other techniques, such as the capability of detecting all the transcripts in one assay over RT-qPCR, such as its higher accuracy and broader dynamic range over microarrays or the ability to detect novel transcripts, including non-coding RNA molecules, at nucleotide-level resolution over both techniques. Despite these advantages, many microbiology laboratories have not yet applied RNA-seq analyses to their investigations. The high cost of the equipment for next-generation sequencing is no longer an issue since this intermediate part of the analysis can be provided by commercial or central services. Here, we detail a protocol for the first part of the analysis, the RNA extraction and an introductory protocol to the bioinformatics analysis of the sequencing data to generate the differential expression results.
10.1007/978-1-0716-3385-4_6
RNA-Seq Data Analysis.
Methods in molecular biology (Clifton, N.J.)
RNA-Seq data analysis stands as a vital part of genomics research, turning vast and complex datasets into meaningful biological insights. It is a field marked by rapid evolution and ongoing innovation, necessitating a thorough understanding for anyone seeking to unlock the potential of RNA-Seq data. In this chapter, we describe the intricate landscape of RNA-seq data analysis, elucidating a comprehensive pipeline that navigates through the entirety of this complex process. Beginning with quality control, the chapter underscores the paramount importance of ensuring the integrity of RNA-seq data, as it lays the groundwork for subsequent analyses. Preprocessing is then addressed, where the raw sequence data undergoes necessary modifications and enhancements, setting the stage for the alignment phase. This phase involves mapping the processed sequences to a reference genome, a step pivotal for decoding the origins and functions of these sequences.Venturing into the heart of RNA-seq analysis, the chapter then explores differential expression analysis-the process of identifying genes that exhibit varying expression levels across different conditions or sample groups. Recognizing the biological context of these differentially expressed genes is pivotal; hence, the chapter transitions into functional analysis. Here, methods and tools like Gene Ontology and pathway analyses help contextualize the roles and interactions of the identified genes within broader biological frameworks. However, the chapter does not stop at conventional analysis methods. Embracing the evolving paradigms of data science, it delves into machine learning applications for RNA-seq data, introducing advanced techniques in dimension reduction and both unsupervised and supervised learning. These approaches allow for patterns and relationships to be discerned in the data that might be imperceptible through traditional methods.
10.1007/978-1-0716-3918-4_18
Single-cell RNA-Seq reveals a highly coordinated transcriptional program in mouse germ cells during primordial follicle formation.
He Yuanlin,Chen Qiuzhen,Dai Juncheng,Cui Yiqiang,Zhang Chi,Wen Xidong,Li Jiazhao,Xiao Yue,Peng Xiaoxu,Liu Mingxi,Shen Bin,Sha Jiahao,Hu Zhibin,Li Jing,Shu Wenjie
Aging cell
The assembly of primordial follicles in mammals represents one of the most critical processes in ovarian biology. It directly affects the number of oocytes available to a female throughout her reproductive life. Premature depletion of primordial follicles contributes to the ovarian pathology primary ovarian insufficiency (POI). To delineate the developmental trajectory and regulatory mechanisms of oocytes during the process, we performed RNA-seq on single germ cells from newborn (P0.5) ovaries. Three cell clusters were classified which corresponded to three cell states (germ cell cyst, cyst breakdown, and follicle) in the newborn ovary. By Monocle analysis, a uniform trajectory of oocyte development was built with a series of genes showed dynamic changes along the pseudo-timeline. Gene Ontology term enrichment revealed a significant decrease in meiosis-related genes and a dramatic increase in oocyte-specific genes which marked the transition from a germ cell to a functional oocyte. We then established a network of regulons by using single-cell regulatory network inference and clustering (SCENIC) algorithm and identified possible candidate transcription factors that may maintain transcription programs during follicle formation. Following functional studies further revealed the differential regulation of the identified regulon Id2 and its family member Id1, on the establishment of primordial follicle pool by using siRNA knockdown and genetic modified mouse models. In summary, our study systematically reconstructed molecular cascades in oocytes and identified a series of genes and molecular pathways in follicle formation and development.
10.1111/acel.13424