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Characterization of Sus scrofa small RNA sequences present in both female and male gonads

ABSTRACT: We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads

ORGANISM(S): Sus scrofa

PROVIDER: GSE57414 | GEO | 2014/07/27

SECONDARY ACCESSION(S): PRJNA246414

REPOSITORIES: GEO

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Characterization of Sus scrofa small RNA sequences present in both female and male gonads

Project description:We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads Determination miRNA, piRNA and tRF expression in swine gonads

2014-07-27 | E-GEOD-57414 | biostudies-arrayexpress

Sus scrofa

Project description:Characterization of Sus scrofa small RNA sequences present in both female and male gonads

| PRJNA246414 | ENA

Zebrafish germline small RNAs

Project description:Piwi proteins specify an animal-specific subclass of the Argonaute family, that in vertebrates are specifically expressed in germ cells. We demonstrate that zebrafish Piwi (Ziwi) is expressed in both the male and the female gonad, and is a component of a germline specifying structure, called nuage. Loss of Ziwi function results in a progressive loss of germ cells due to apoptosis during larval development. In animals that have only reduced Ziwi function, germ cells are maintained, but display abnormal levels of apoptosis in adults. In mammals, Piwi proteins have been found to associate with approximately 29-nucleotide long, testis specific RNA molecules, called piRNAs. Here we show that zebrafish piRNAs are present in both ovaries and testes. Furthermore, we show that piRNAs are modified at their 3’ end and that they are produced by a Dicer independent mechanism. Many ovarian piRNAs are derived from transposons, implicating a role for these molecules in the silencing of these repetitive elements in vertebrates. Keywords: high-throughput 454 sequencing sequencing of ~30 nt small RNAs from zebrafish ovaries and testes using 454 technology

2007-04-04 | E-GEOD-7131 | biostudies-arrayexpress

Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads

Project description:Whereas in ovo exposure of genetically male (ZZ) chicken embryos to exogenous estrogens temporarily feminizes gonads at the time of hatching, the morphologically ovarian ZZ-gonads (FemZZs for feminized ZZ gonads) are masculinized back to testes within one year. To identify the feminization-resistant “memory” of genetic male sex, FemZZs showing varying degrees of feminization were subjected to transcriptomic, DNA methylome, and immunofluorescence analyses. Protein-coding genes were classified based on their relative mRNA expression across normal ZZ-testes, genetically female (ZW) ovaries, and FemZZs. We identified a group of 25 genes that were strongly expressed in both ZZ-testes and FemZZs but dramatically suppressed in ZW-ovaries. Interestingly, 84% (21/25) of these feminization-resistant testicular marker genes, including the DMRT1 master masculinizing gene, were located in chromosome Z. Expression of representative marker genes of germline cells (e.g., DAZL or DDX4/VASA) was stronger in FemZZs than normal ZZ-testes or ZW-ovaries. We also identified 231 repetitive sequences (RSs) that were strongly expressed in both ZZ-testes and FemZZs, but these RSs were not enriched in chromosome Z. Although 94% (165/176) of RSs exclusively expressed in ZW-ovaries were located in chromosome W, no feminization-inducible RS was detected in FemZZs. DNA methylome analysis distinguished FemZZs from normal ZZ- and ZW-gonads. Immunofluorescence analysis of FemZZ gonads revealed expression of DMRT1 protein in medullary SOX9+ somatic cells and apparent germline cell populations in both medulla and cortex. Taken together, our study provides evidence that both somatic and germline cell populations in morphologically feminized FemZZs maintain significant transcriptomic and epigenetic memories of genetic sex.

2020-10-31 | GSE160494 | GEO

Expression data from Mouse embryo

Project description:Mice lacking the function of the PcG protein CBX2 (also known as M33) show defects in gonadal, adrenal, and splenic development. In particular, XY knockout mice develop ovaries but not testes, and the gonads are hypoplastic in both sexes. To clarify the molecular basis of the defects, RNA prepared from both wild type and KO gonads were subjected to microarray analyses.

2011-07-01 | GSE29485 | GEO

Sus scrofa scrofa

Project description:Transcriptomic analysis in ovaries of Chinese Erhualian sows

| PRJNA312567 | ENA

Transcriptional signature of the developing rat testes and ovaries following embryonic exposure to 2,3,7,8-TCDD

Project description:We determined global gene changes in immature ovaries and testes in response to an in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure. Microarray analysis was performed using testes and ovaries of the dioxin-exposed dams’ offspring. One hundred and thirteen genes were differentially expressed in ovaries and 56 genes in testes of 14 and 5 days-old, respectively. Real-time PCR was used to validate and extend data using RNA extracted from 5 to 145-day old rat testes and 3 to 25-day old rat ovaries. A single gene of the classic dioxin battery, i.e., the repressor of the aryl hydrocarbon receptor (Ahrr) was found altered in testes. In contrast, several of them including Cyp1a1, Cyp1b1, Nqo1, and Ahrr were found up-regulated in ovary, pituitary (a different endocrine organ) and liver. In addition to Ahrr, we identified 6 genes targeted by dioxin in both gonads, including the chemokines Cxcl4, Ccl5. Ccl5 gene expression levels were also regulated in pituitary and liver, so as pituitary Cxcl4. Four genes targeted by TCDD in testis and meeting stringent criteria were further surveyed. It included 2 genes with no previous reported function in testis, Art2b, Gzmf, Hpgds and Fgf13. Fgf13 was down-regulated in testis, and pituitary but not in ovary or liver. Interestingly, Art2b and Gzmf were up-regulated in testis, liver and pituitary but not ovary. Finally, Hpgds was unique in that expressed in various tissues it was regulated by TCDD in the gonads but not in the other tissues studied. Transcriptomic analysis on testes at 5 days and in ovaries at 14 days. In both cases, 3 rats treated in utero by TCDD were compared to 3 rats treated with sesame-oil vehicle

2011-10-11 | E-GEOD-32890 | biostudies-arrayexpress

DH06 Adrenal ACTH Sus scrofa

Project description:Large White and Meishan pigs were either non-treated or injected with mammalian 1-24 ACTH (Immediate Synachten, Novartis France) at the dose of 250 µg per animal. Pigs were sacrificed either immediately after capture from their home cage (non-treated animals) or 1 hour following ACTH injection. Adrenal glands were immediately collected from pigs and frozen on dry ice and then stored at -80°C until RNA isolation. Keywords: stress response, adrenal, gene expression, pig

2008-01-07 | GSE8377 | GEO

pCADD: SNV prioritisation in Sus scrofa.

Project description: Not available

| S-EPMC7006094 | biostudies-literature

Comparative analysis of piRNA profiles reveals cryoinjury or freezability between boar (Sus scrofa) and giant panda (Ailuropoda melanoleuca) sperm during cryopreservation

Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.

2021-04-19 | GSE163128 | GEO

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