MicroRNA and piRNA profiles in normal human testis
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REPOSITORIES: ENA
Dataset's files
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| ERR328151.fastq.gz | Fastqsanger.gz |
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Project description:We employed Solexa sequencing technology to profile miRNAs and piRNA in normal human testis, three cases, pulled together
2014-01-21 | E-MTAB-1629 | biostudies-arrayexpress
Project description:BackgroundMicroRNAs (miRNAs) are the class of small endogenous RNAs that play an important regulatory role in cells by negatively affecting gene expression at transcriptional and post-transcriptional levels. There have been extensive studies aiming to discover miRNAs and to analyze their functions in the cells from a variety of species. However, there are no published studies of miRNA profiles in human testis using next generation sequencing (NGS) technology.ResultsWe employed Solexa sequencing technology to profile miRNAs in normal human testis. Total 770 known and 5 novel human miRNAs, and 20121 piRNAs were detected, indicating that the human testis has a complex population of small RNAs. The expression of 15 known and 5 novel detected miRNAs was validated by qRT-PCR. We have also predicted the potential target genes of the abundant known and novel miRNAs, and subjected them to GO and pathway analysis, revealing the involvement of miRNAs in many important biological phenomenon including meiosis and p53-related pathways that are implicated in the regulation of spermatogenesis.ConclusionsThis study reports the first genome-wide miRNA profiles in human testis using a NGS approach. The presence of large number of miRNAs and the nature of their target genes suggested that miRNAs play important roles in spermatogenesis. Here we provide a useful resource for further elucidation of the regulatory role of miRNAs and piRNAs in the spermatogenesis. It may also facilitate the development of prophylactic strategies for male infertility.
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Project description:Testicular germ cell tumours (TGCTs) of young adult men, seminoma (SEM) and nonseminoma (NSEM), develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it to the miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only (SCO) that lack germ cells, testis tumours (SEM and embryonal carcinoma, EC; an undifferentiated component of NSEM) and foetal male and female gonads. Principal component analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads, and testis tumours. These included miRNAs from the hsa-miR-371~373 and -302~367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and the hsa-miR-182~183~96 cluster were highly expressed in SEM, while the hsa-miR-515~526 cluster was high in EC. We conclude that miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes.
2011-11-01 | GSE31824 | GEO
Project description:Testicular germ cell tumours (TGCTs) of young adult men, seminoma (SEM) and nonseminoma (NSEM), develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it to the miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only (SCO) that lack germ cells, testis tumours (SEM and embryonal carcinoma, EC; an undifferentiated component of NSEM) and foetal male and female gonads. Principal component analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads, and testis tumours. These included miRNAs from the hsa-miR-371~373 and -302~367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and the hsa-miR-182~183~96 cluster were highly expressed in SEM, while the hsa-miR-515~526 cluster was high in EC. We conclude that miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes. We used Agilent microarrays to determine the expression of microRNAs in samples from testis. We first used Agilent-016436 Human miRNA Microarray 1.0 G4472A (GPL9081; miRNA ID version) on 4 samples: normal testis, testis with 30% carcinoma in situ (CIS) tubules, testis with 50% CIS tubules and testis with 99-100% CIS tubules. This allowed us to determine the correlation between miRNA expressiona and the content of CIS cells in the samples. This is the file with data from those four arrays. Next, we used Agilent-019118 Human miRNA Microarray 2.0 G4470B (GPL8936; Probe Name version) on 24 samples that included normal testis, testis with the precursor for testis cancer carcinoma in situ (CIS), Sertoli-cell-only testis (contains the somatic testis cells but no germ cells), seminom and non-seminom tumours, and foetal gonads. This constitute the main part of the experiment and the publication, but the data was submitted to GEO in an independent file.
2011-11-01 | E-GEOD-31824 | biostudies-arrayexpress
Project description:In developing male germ cells, prospermatogonia, two Piwi proteins, MILI and MIWI2, use piRNA guides to repress transposable element (TE) expression and ensure genome stability and proper gametogenesis. In addition to their roles in post-transcriptional TE repression, both proteins are required for DNA methylation of TE sequences. Here we analyzed the effect of Miwi2 deficiency on piRNA biogenesis and transposon repression. Miwi2-deficiency had only a minor impact on piRNA biogenesis; however, the piRNA profile of Miwi2-knockout mice indicated overexpression of several LINE1 TE families that led to activation of the ping-pong piRNA cycle. Furthermore, we found that MILI and MIWI2 have distinct functions in TE repression in the nucleus. MILI is responsible for DNA methylation of a larger subset of TE families than MIWI2 suggesting that the proteins have independent roles in establishing DNA methylation patterns. Small RNA profiles (19-30 nt range) of embryonic (E16.5) and post-natal (P10) testis of Miwi2 mutant mice and matched heterozygote controls. mRNA profiles of embryonic testis (E16.5) of heterozygote control mice and of postnatal testis (P10) of Miwi2 and Mili mutants and heterozygote controls. CpG methylation BS-seq profile of postnatal (P10) spermatocytes of Miwi2 mutant mice and matched heterozygote controls.
2015-07-11 | E-GEOD-70731 | biostudies-arrayexpress
Project description:Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA were implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in Drosophila ovarian follicle cells. Previous studies further reported the presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA in mouse tissues and human NK cells. Here, by analyzing high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples, we show widespread presence of pilRNA displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. These findings indicate that piRNA-like molecules might play important roles outside of the germline. Small RNA expression profiles were examined in five rhesus macaque tissues (testis, epididymis, prostate, seminal vesicles, cortex) and one mouse tissue (epididymis).
2011-06-01 | E-GEOD-27369 | biostudies-arrayexpress
Project description:Pregnant females were distributed into two experimental groups: control group and MC-LR group which were exposed to 0 and 10 μg/L of MC-LR through drinking water separately during fetal and lactational periods. In 30 days old, the animals were euthanized. Testes were determined to investigate the different expressions of piRNAs using a piRNA microarray.
2016-10-13 | GSE87876 | GEO