Evolution of an X-linked miRNA family predominately expressed in mammalian male germ cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA395954 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5874000.fastq.gz | Fastqsanger.gz | |||
| SRR5874010.fastq.gz | Fastqsanger.gz | |||
| SRR5873991.fastq.gz | Fastqsanger.gz | |||
| SRR5874001.fastq.gz | Fastqsanger.gz | |||
| SRR5874011.fastq.gz | Fastqsanger.gz |
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Project description:microRNAs (miRNAs) are important post-transcriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during spermatogenesis in mammals is lacking. In the present study, we sequenced small RNAs in highly purified spermatogonial stem cells (SSCs), spermatocytes in the pre-leptotene, leptotene, zygotene and pachytene stages, haploid round spermatids and spermatozoa. We found that a family of X-linked miRNAs, named spermiRs, is predominantly expressed in spermatogonia and early meiotic phases. Profiling of small RNAs in different mammalian tissues revealed a conserved high expression pattern of spermiRs in testes. spermiR appears to originate from THER1 in marsupial, a retrotransposon that is extinct in current mammals. It has expanded rapidly and has diversified into two clusters, spermiR-L and spermiR-R, by tandem duplication, which was partially mediated by flanking retrotransposable elements. Notably, despite the highly frequent lineage-specific duplication events, all spermiR family members are strictly located between two conserved protein coding genes, Slitrk2 and Fmr1. Intriguingly, spermiR-Ls and spermiR-Rs have evolved different expression preferences during spermatogenesis in different mammals. Moreover, the sequences of spermiRs and their precursors, including the seed regions, are highly divergent within and among mammals. However, their target genes are largely overlapping in male reproduction-related pathways. When miR-741, the most highly expressed spermiRs during mouse spermatogenesis, was knocked out in SSCs, another spermiR, miR-465, was dramatically up-regulated and became the most abundant one, indicating functional compensation between spermiR family members. All these observations indicate a strong co-evolution between spermiRs and their targets.
2019-01-19 | GSE101933 | GEO
Project description:MicroRNAs (miRNAs) are important posttranscriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during mammalian spermatogenesis are lacking. Herein, we sequenced small RNAs in highly purified mouse spermatogenic cells at different stages. We found that a family of X-linked miRNAs named spermatogenesis-related miRNAs (spermiRs) is predominantly expressed in the early meiotic phases and has a conserved testis-specific high expression pattern in different mammals. We identified one spermiR homolog in opossum; this homolog might originate from THER1, a retrotransposon that is active in marsupials but extinct in current placental mammals. SpermiRs have expanded rapidly with mammalian evolution and are diverged into two clades, spermiR-L and spermiR-R, which are likely to have been generated at least in part by tandem duplication mediated by flanking retrotransposable elements. Notably, despite having undergone highly frequent lineage-specific duplication events, the sequences encoding all spermiR family members are strictly located between two protein-coding genes, Slitrk2 and Fmr1. Moreover, spermiR-Ls and spermiR-Rs have evolved different expression patterns during spermatogenesis in different mammals. Intriguingly, the seed sequences of spermiRs, which are critical for the recognition of target genes, are highly divergent within and among mammals, whereas spermiR target genes largely overlap. When miR-741, the most highly expressed spermiR, is knocked out in cultured mouse spermatogonial stem cells (SSCs), another spermiR, miR-465a-5p, is dramatically upregulated and becomes the most abundant miRNA. Notably, miR-741-/- SSCs grow normally, and the genome-wide expression levels of mRNAs remain unchanged. All these observations indicate functional compensation between spermiR family members and strong coevolution between spermiRs and their targets.
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Project description:In the mouse, germ cells and embryonic stem cells maintain an epigenetically poised (bivalent) state, defined by the simultaneous presence of the opposing histone modifications H3K4me3 and H3K27me3 and by transcriptional repression, at the promoters of many developmental regulatory genes. We compared genome-wide chromatin state in male germ cells of five mammalian and one avian species. We identified a set of 405 genes whose promoters retain poised chromatin in the mammalian germ line throughout mammalian evolution.
2016-05-07 | GSE68507 | GEO
Project description:We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis using High Density Oligonucleotide Microarrays and highly enriched cell populations. Among 11955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages as compared to total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic and post-meiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic and/or post-meiotic germ cells of 293 as yet uncharacterized transcripts some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains numerous potential germ cell specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at http://www.germonline.org.
2004-03-01 | E-MEXP-31 | biostudies-arrayexpress
Project description:Homeobox genes encode transcription factors that function in various developmental processes and are usually evolutionarily conserved in their sequences. However, two X-chromosome-linked testis-expressed homeobox genes, one from rodents and the other from fruit flies, are known to evolve rapidly under positive Darwinian selection. Here we report yet another case, from primates. TGIFLX is an X-linked homeobox gene that originated by retroposition of the autosomal gene TGIF2, most likely in a common ancestor of rodents and primates. While TGIF2 is ubiquitously expressed, TGIFLX is exclusively expressed in adult testis. A comparison of the TGIFLX sequences among 16 anthropoid primates revealed a significantly higher rate of nonsynonymous nucleotide substitution (d(N)) than synonymous substitution (d(S)), strongly suggesting the action of positive selection. Although the high d(N)/d(S) ratio is most evident outside the homeobox, the homeobox has a d(N)/d(S) of approximately 0.89 and includes two codons that are likely under selection. Furthermore, the rate of radical amino acid substitutions that alter amino acid charge is significantly greater than that of conservative substitutions, suggesting that the selection promotes diversity of the protein charge profile. More interestingly, an analysis of 64 orthologous homeobox genes from humans and mice shows substantially higher rates of amino acid substitution in X-linked testis-expressed genes than in other genes. These results suggest a general pattern of rapid evolution of mammalian X-linked testis-expressed homeobox genes. Although the physiological function of and the exact selective agent on TGIFLX and other rapidly evolving homeobox genes are unclear, the common expression pattern of these transcription factor genes led us to conjecture that the selection is related to one or more aspects of male reproduction and may contribute to speciation.
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Project description:We report the whole-transcriptome profile with total RNA sequencing of postnatal male germ cells. Histone modification levels are dynamically controlled during mammalian spermatogenesis. We found that H3K9 demethylases, Jmjd1a and Jmjd1b catalyze H3K9 demethylation in prospermatogonia. Combined loss of Jmjd1 enzymes disturbed prospermatogonia to spermatogonia transition in mice. To examine a role of Jmjd1 in prospermatogonia to spermatogonia transition, we performed RNA-seq and ChIP-seq analyses using postnatal germ cells at P3 and P7.
2020-06-08 | GSE148053 | GEO
Project description:Resolving the 3D landscape of transcription-linked mammalian chromatin folding
| PRJNA535430 | ENA
Project description:We report the H3K9me2 distribution profile with ChIP sequencing of postnatal male germ cells. Histone modification levels are dynamically controlled during mammalian spermatogenesis. We found that H3K9 demethylases, Jmjd1a and Jmjd1b catalyze H3K9 demethylation in prospermatogonia. Combined loss of Jmjd1 enzymes disturbed prospermatogonia to spermatogonia transition in mice. To examine a role of Jmjd1 in prospermatogonia to spermatogonia transition, we performed RNA-seq and ChIP-seq analyses using postnatal germ cells at P3 and P7.
2020-06-08 | GSE148054 | GEO
Project description:Mammalian spermatogenesis occurs in a precise and coordinated manner in the seminiferous tubules. One of the attempts to understand the detailed biological process during mammalian spermatogenesis at the molecular level has been to identify the testis specific genes followed by study of the testicular expression pattern of the genes. From the subtracted cDNA library of rat testis prepared using representational difference analysis (RDA) method, a complimentary DNA clone encoding type III member of a DnaJ family protein, DnaJC18, was cloned (GenBank Accession No. DQ158861). The full-length DnaJC18 cDNA has the longest open reading frame of 357 amino acids. Tissue and developmental Northern blot analysis revealed that the DnaJC18 gene was expressed specifically in testis and began to express from postnatal week 4 testis, respectively. In situ hybridization studies showed that DnaJC18 mRNA was expressed only during the maturation stages of late pachy- tene, round and elongated spermatids of adult rat testis. Western blot analysis with DnaJC18 antibody revealed that 41.2 kDa DnaJC18 protein was detected only in adult testis. Immunohistochemistry study further confirmed that DnaJC18 protein, was expressed in developing germ cells and the result was in concert with the in situ hybridization result. Confocal microscopy with GFP tagged DnaJC18 protein revealed that it was localized in the cytoplasm of cells. Taken together, these results suggested that testis specific DnaJC18, a member of the type III DnaJ protein family, might play a role during germ cell maturation in adult rat testis.
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Project description:Transcriptional Metabolic Reprograming Drives Meiotic Fate Decision in Mammalian Germ Cells
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