Control of human testis-specific gene expression.
Brown Jay C
PloS one
BACKGROUND:As a result of decades of effort by many investigators we now have an advanced level of understanding about several molecular systems involved in the control of gene expression. Examples include CpG islands, promoters, mRNA splicing and epigenetic signals. It is less clear, however, how such systems work together to integrate the functions of a living organism. Here I describe the results of a study to test the idea that a contribution might be made by focusing on genes specifically expressed in a particular tissue, the human testis. EXPERIMENTAL DESIGN:A database of 239 testis-specific genes was accumulated and each was examined for the presence of features relevant to control of gene expression. These include: (1) the presence of a promoter, (2) the presence of a CpG island (CGI) within the promoter, (3) the presence in the promoter of a transcription factor binding site near the transcription start site, (4) the level of gene expression, and (5) the above features in genes of testis-specific cell types such as spermatocyte and spermatid that differ in their extent of differentiation. RESULTS:Of the 107 database genes with an annotated promoter, 56 were found to have one or more transcription factor binding sites near the transcription start site. Three of the binding sites observed, Pax-5, AP-2αA and GRα, stand out in abundance suggesting they may be involved in testis-specific gene expression. Compared to less differentiated testis-specific cells, genes of more differentiated cells were found to be (1) more likely to lack a CGI, (2) more likely to lack introns and (3) higher in expression level. The results suggest genes of more differentiated cells have a reduced need for CGI-based regulatory repression, reduced usage of gene splicing and a smaller set of expressed proteins.
10.1371/journal.pone.0215184
Functional analysis of human cancer-associated genes and their association with the testes and epididymis.
Hua Xiu-Feng,Wang Xue-Bo,Liu Fu-Jun
Oncology letters
Human cancer-associated UniGene sets (NCBI GeneBank) provide a platform for identifying differentially-expressed genes in human cancers. The present study identified and characterized a set of human cancer-associated genes using the Digital Differential Display (DDD) and functional analysis tools. A total of 1,904 genes were differentially expressed in 15 cancer types, including genes that had been previously shown to be specific in certain human cancers. A total of 274 genes were uniquely expressed in certain cancer types, including 37 genes that were highly expressed in the human testes and epididymis. These genes mainly functioned as ribosomal proteins, enzymes, receptors, secretory proteins and cell adhesion molecules. The most common domains that were encoded by the cancer-associated genes were those of cytochrome P450 CYP2D6, serpin and apolipoprotein A-I. A further gene ontology (GO) enrichment analysis revealed seven major functional clusters, which corresponded to the enriched pathways involved in cancer. The present study provides a source of cancer-associated genes and their functions. The results provide new insights into cancer biology and the involvement of highly-expressed epididymal genes in cancer biomarkers.
10.3892/ol.2013.1450
Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.
Zhu Jinhang,Chen Geng,Zhu Sibo,Li Suqing,Wen Zhuo,Bin Li ,Zheng Yuanting,Shi Leming
Scientific reports
Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.
10.1038/srep28400
An integrated bioinformatics analysis of mouse testis protein profiles with new understanding.
Liu FuJun,Wang HaiYan,Li JianYuan
BMB reports
The testis is major male gonad responsible for spermatogenesis and steroidogenesis. Much knowledge is still remained to be learned about the control of these events. In this study, we performed a comprehensive bioinformatics analysis on 1,196 mouse testis proteins screened from public protein database. Integrated function and pathway analysis were performed through Database for Annotation, Visualization and Integrated Discovery (DAVID) and ingenuity Pathway Analysis (IPA), and significant features were clustered. Protein membrane organization and gene density on chromosomes were analyzed and discussed. The enriched bioinformatics analysis could provide clues and basis to the development of diagnostic markers and therapeutic targets for infertility and male contraception.
10.5483/BMBRep.2011.44.5.347
Characteristics of 292 testis-specific genes in human.
Tang Aifa,Yu Zhendong,Gui Yaoting,Zhu Hui,Zhang Libin,Zhang Jianrong,Cai Zhiming
Biological & pharmaceutical bulletin
To explore their genomic and functional characteristics, 292 human testis-specific genes were obtained from a UniGene library and a full-scale analysis was made. Various bioinformatics tools were applied to analyze the gene ontology and chromosome location, and the expression profiles of eight selected candidates from the 292 genes were analyzed using RT-PCR for 12 adult human tissues. The results showed that of the total 292 genes, 153 were known (114 assigned genes and 39 named genes), and 139 were unknown. Of the 114 assigned genes, 63 were labeled to molecular function, 28 to cellular component, 23 to biological process. All 292 genes are distributed on human chromosomes at different gene density, lower gene density appears on chromosomes 21 (R=0.22), X (R=0.33), 14 (R=0.39), 10 (R=0.61), 8 (R=0.63), and 18 (R=0.67) and higher density on chromosomes 19 (R=3.65), 20 (R=1.83), 16 (R=1.74), and 17 (R=1.64). The expression profile of the eight selected genes in the 12 human tissues showed that five candidate genes: Hs.443729, Hs.115366, Hs.558087, Hs.534501, and Hs.132104 were expressed exclusively in human testis; Hs.132310, Hs.443299 were expressed highly in testis and also expressed weakly in human heart; Hs.160370 was expressed in human testis, ovary, uterus, and not expressed in other tissues. Our study can be a basis for characterization of the function of human testis-specific genes during male mammalian spermatogenesis.
10.1248/bpb.30.865
Comparative and functional analysis of testis-specific genes.
Liu FuJun,Jin ShaoHua,Li Ning,Liu Xin,Wang HaiYan,Li JianYuan
Biological & pharmaceutical bulletin
The testis is the special male gonad responsible for spermatogenesis and steroidogenesis with complex gene expressions. Characterizing and comparing the testis-specific genes in different species can reveal key genes related to testis specific functions and provide supplementary information for study of human testis function. We screened testis-specific genes from Unigene libraries, total 317, 449 and 147 testis-specific genes were identified for human, mouse and rat, respectively. Ten from thirteen selected human testis-specific genes were validated exclusively expressed in the testis by reverse transcription polymerase chain reaction (RT-PCR). Systematic bioinformatics analysis showed that specific genes were mainly related to spermatogenesis and testis development process with significant Glycolysis and Pyruvate metabolism. Enrichment functions were discussed.
10.1248/bpb.34.28