In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures
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ABSTRACT:
ORGANISM(S): Mus musculus Bos taurus
PROVIDER: GSE81490 | GEO | 2016/12/15
SECONDARY ACCESSION(S): PRJNA321745
REPOSITORIES: GEO
Similar Datasets
Project description:In mammals, male fate is under the control of the master transcriptional regulator, SOX9: in its presence, somatic precursor cells of the embryonic gonads differentiate into Sertoli cells, the main organizers of testicular differentiation. Therefore, analyzing target genes of this transcription factor allows understanding mechanisms of cellular commitment at the genomic level. With the use of ChIP-seq in murine and bovine wild-type testes combined with RNAseq from mouse testes lacking SOX9, we identified SOX9 target genes in the mammalian fetal gonad. SOX9 in murine and bovine fetal testes binds to a large set of genes conserved among mammals, including those with well-established roles in testis and ovary development. RNAseq analysis shows that testis and ovary display sex specific RNA splicing and that SOX9 mediates both target gene transcription and differential splicing. Regions bound by SOX9 are predominantly 5’ proximal or intra-genic, and display a specific genomic features that we call "Sertoli cell signatures" or SCS. The SCS is conserved among mammals and comprises multiple binding motifs for the Sertoli reprogramming factors SOX9, GATA4 and DMRT1; indeed, independent DMRT1 ChIP-seq confirms the enrichment of the SCS. Bioinformatic analysis of SCSs regions predicts novel regulatory mechanisms prompting functional validation. For example, we detected SCS in target genes of the nuclear factor TRIM28 and we show experimentally that SOX9 and TRIM28 proteins interact in fetal testis.
2016-12-15 | GSE81489 | GEO
Project description:In mammals, male fate is under the control of the master transcriptional regulator, SOX9: in its presence, somatic precursor cells of the embryonic gonads differentiate into Sertoli cells, the main organizers of testicular differentiation. Therefore, analyzing target genes of this transcription factor allows understanding mechanisms of cellular commitment at the genomic level. With the use of ChIP-seq in murine and bovine wild-type testes combined with RNAseq from mouse testes lacking SOX9, we identified SOX9 target genes in the mammalian fetal gonad. SOX9 in murine and bovine fetal testes binds to a large set of genes conserved among mammals, including those with well-established roles in testis and ovary development. RNAseq analysis shows that testis and ovary display sex specific RNA splicing and that SOX9 mediates both target gene transcription and differential splicing. Regions bound by SOX9 are predominantly 5’ proximal or intra-genic, and display a specific genomic features that we call "Sertoli cell signatures" or SCS. The SCS is conserved among mammals and comprises multiple binding motifs for the Sertoli reprogramming factors SOX9, GATA4 and DMRT1; indeed, independent DMRT1 ChIP-seq confirms the enrichment of the SCS. Bioinformatic analysis of SCSs regions predicts novel regulatory mechanisms prompting functional validation. For example, we detected SCS in target genes of the nuclear factor TRIM28 and we show experimentally that SOX9 and TRIM28 proteins interact in fetal testis.
2016-12-15 | GSE81488 | GEO
Project description:In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures
| PRJNA321745 | ENA
Project description:In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures [ChIP-seq]
| PRJNA321750 | ENA
Project description:In mammalian embryonic gonads, SOX9 is required for the determination of Sertoli cells that orchestrate testis morphogenesis. To identify genetic networks directly regulated by SOX9, we combined analysis of SOX9-bound chromatin regions from murine and bovine foetal testes with sequencing of RNA samples from mouse testes lacking Sox9. We found that SOX9 controls a conserved genetic programme that involves most of the sex-determining genes. In foetal testes, SOX9 modulates both transcription and directly or indirectly sex-specific differential splicing of its target genes through binding to genomic regions with sequence motifs that are conserved among mammals and that we called 'Sertoli Cell Signature' (SCS). The SCS is characterized by a precise organization of binding motifs for the Sertoli cell reprogramming factors SOX9, GATA4 and DMRT1. As SOX9 biological role in mammalian gonads is to determine Sertoli cells, we correlated this genomic signature with the presence of SOX9 on chromatin in foetal testes, therefore equating this signature to a genomic bar code of the fate of foetal Sertoli cells. Starting from the hypothesis that nuclear factors that bind to genomic regions with SCS could functionally interact with SOX9, we identified TRIM28 as a new SOX9 partner in foetal testes.
| S-EPMC5499551 | biostudies-literature
Project description:A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination.
| S-EPMC3440412 | biostudies-literature
Project description:ER71, also known as ETV2, is an ETS transcription factor that is expressed during embryogenesis and in adult testes. We show that Er71 transcription can be up-regulated by SRY, the key determinant of male differentiation. Accordingly, SRY bound to and activated the Er71 promoter, and mutation of a putative SRY binding site abolished this promoter activation. In turn, ER71 was able to bind to the promoter of Sox9, the primary target of SRY and a critical transcription factor for maintenance of the Sertoli cell phenotype. Mutation of the ER71 binding site in the Sox9 promoter suppressed ER71-dependent up-regulation of Sox9 transcription, and a dominant-negative ER71 molecule severely reduced Sox9 transcription in a Sertoli cell line. Conversely, SOX9 bound the Er71 promoter in vivo and Sox9 down-regulation reduced Er71 transcript levels. Together, these data suggest a mechanism by which SRY induces Sox9 and Er71 transcription early in testis differentiation, whereas ER71 and SOX9 participate in an autoregulatory loop to sustain each other's expression after Sry expression has subsided in mice. Thereby, ER71 and SOX9 may affect late testis development as well as the function of the adult male gonad.
| S-EPMC3390640 | biostudies-literature
Project description:In almost all vertebrates, the downstream of the sox9 signaling axis is well conserved for testis differentiation. The upstream genes of this pathway vary from species to species during evolution. Yet, little is known about how these signaling cascades are regulated and what cellular processes are dominant in ovary-testis transformation in juvenile zebrafish. In this study, we find that the transforming gonads undergo activation of sox9a-expressing stromal cells with increased deposition of extracellular matrix and formation of degenerative compartments. This leads to follicle disassembly, oocyte degeneration, follicle cell-cyp19a1a-amh conversions, and, eventually, formation of the testis cord. In vitro primary culture of juvenile ovary tissue in gonadotropins increases cytoplasmic accumulation of sox9a and p-Erk1/2, and induces mesenchymal morphology. MAPK inhibitors (MKI), a mixture of PD98059 and U0216, eliminate the cytoplasmic distribution but do not eradicate nuclear localization of sox9a and p-Erk1/2. Nuclear p53 are relatively increased in MKI-treated cells that exhibit less spreading and reduced proliferation. Despite uniform nuclear condensation, only a fraction of cells displayed the apoptotic phenotype. These results suggest that high levels of cytoplasmic sox9a and p-Erk1/2 activity activate stromal cells and enhance the production of extracellular matrix required for testis cord formation, whereas deregulation and translocation of sox9a and p-Erk1/2 induce follicle disassembly and incomplete apoptosis associated with nuclear p53. Together with the established FSH/cAMP/MAPK/AMH pathway in mammalian granulosa and Sertoli cells, we demonstrated that the sox9 axis signaling that determines testis formation in mammals also induces zebrafish ovary-testis transition, and adds to its conserved role in sex reversal.
| S-EPMC3847332 | biostudies-literature
Project description:A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. At embryonic day 13 (E13) of pregnancy rats were euthanized and embryonic gonads were collected for chromatin. A modified ChIP-Chip analysis using a comparative hybridization was used to identify direct downstream binding targets for SRY and for SOX9. Then, bioinformatic analysis of the downstream binding targets was done to identify gene networks and cellular pathways that are potentially involved in the induction of Sertoli cell differentiation and testis development.
2014-12-05 | E-GEOD-63855 | biostudies-arrayexpress
Project description:Ultraconserved regions (UCR) are genomic segments of more than 200 base pairs that are evolutionarily conserved among mammalian species. They are thought to have functions as transcriptional enhancers and regulators of alternative splicing. Recently, it was shown that numerous RNAs are transcribed from these regions. These UCR-encoded transcripts (ucRNAs) were found to be expressed in a tissue- and disease-specific manner and may interfere with the function of other RNAs through RNA: RNA interactions. We hypothesized that ucRNAs have unidentified roles in the pathogenesis of human prostate cancer. In a pilot study, we examined ucRNA expression profiles in human prostate tumors.Using a custom microarray with 962 probesets representing sense and antisense sequences for the 481 human UCRs, we examined ucRNA expression in resected, fresh-frozen human prostate tissues (57 tumors, 7 non-cancerous prostate tissues) and in cultured prostate cancer cells treated with either epigenetic drugs (the hypomethylating agent, 5-Aza 2'deoxycytidine, and the histone deacetylase inhibitor, trichostatin A) or a synthetic androgen, R1881. Expression of selected ucRNAs was also assessed by qRT-PCR and NanoString®-based assays. Because ucRNAs may function as RNAs that target protein-coding genes through direct and inhibitory RNA: RNA interactions, computational analyses were applied to identify candidate ucRNA:mRNA binding pairs.We observed altered ucRNA expression in prostate cancer (e.g., uc.106+, uc.477+, uc.363 + A, uc.454 + A) and found that these ucRNAs were associated with cancer development, Gleason score, and extraprostatic extension after controlling for false discovery (false discovery rate < 5% for many of the transcripts). We also identified several ucRNAs that were responsive to treatment with either epigenetic drugs or androgen (R1881). For example, experiments with LNCaP human prostate cancer cells showed that uc.287+ is induced by R1881 (P < 0.05) whereas uc.283 + A was up-regulated following treatment with combined 5-Aza 2'deoxycytidine and trichostatin A (P < 0.05). Additional computational analyses predicted RNA loop-loop interactions of 302 different sense and antisense ucRNAs with 1058 different mRNAs, inferring possible functions of ucRNAs via direct interactions with mRNAs.This first study of ucRNA expression in human prostate cancer indicates an altered transcript expression in the disease.
| S-EPMC3626580 | biostudies-literature