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Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Sylvain LEMEILLE

PROVIDER: E-GEOD-63130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RFX2 Is a Major Transcriptional Regulator of Spermiogenesis.

Kistler W Stephen WS Baas Dominique D Lemeille Sylvain S Paschaki Marie M Seguin-Estevez Queralt Q Barras Emmanuèle E Ma Wenli W Duteyrat Jean-Luc JL Morlé Laurette L Durand Bénédicte B Reith Walter W

PLoS genetics 20150710 7

Spermatogenesis consists broadly of three phases: proliferation of diploid germ cells, meiosis, and finally extensive differentiation of the haploid cells into effective delivery vehicles for the paternal genome. Despite detailed characterization of many haploid developmental steps leading to sperm, only fragmentary information exists on the control of gene expression underlying these processes. Here we report that the RFX2 transcription factor is a master regulator of genes required for the hap ...[more]

PMID: 26162102

Similar Datasets

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: DNA was extracted from decapsulated testes of 21 day old mice. ChIP sequencing was used to determine the binding sites of RFX2. Results: ChIP-Seq analysis identified ~880 binding sites of RFX2 near TSS. Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function. Testicular RFX2 binding sites were determined by deep sequencing using testes from 2 independentWT mice

2015-11-02 | E-GEOD-68282 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes at post natal day 30 [RNA-Seq P30]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 29-30 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 640 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~150 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 640 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function. Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 4 independent Rfx2-/- mice

2015-11-02 | E-GEOD-68283 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes at post natal day 21 [RNA-Seq P21]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 21 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 105 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~50 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function. Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 6 independent Rfx2-/- mice

2015-11-02 | E-GEOD-68284 | biostudies-arrayexpress

NLRC5 specifically transactivates MHC class I and related genes through a distinctive SXY module

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2015-02-27 | E-GEOD-59092 | biostudies-arrayexpress

Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing

Project description:Dendritic-cell (DC) maturation involves substantial remodeling of their gene-expression program. Most research has focused on inducible gene-expression networks promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC-function by inducing gene silencing remain poorly understood. Here we describe a novel primary epigenetic-silencing response that makes major contributions to the DC-maturation process. The repressed genes function in pivotal processes - including antigen-presentation, extracellular-signal detection, signal-transduction and lipid-mediator biosynthesis - underscoring the central contribution of the silencing mechanism to rapid reshaping of DC-function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this transcription factor in marking genes poised for inducible repression Analysis of PU.1 binding sites in mo-DC

2015-01-01 | E-GEOD-58864 | biostudies-arrayexpress

Coordinated genomic control of ciliogenesis and cell movement by Rfx2

Project description:We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of Rfx2-regulated transcripts and chromosomal binding sites, we provide a comprehensive accounting of the target genes by which Rfx2 controls ciliogenesis and cilia beating in vertebrates. RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control

2013-12-12 | E-GEOD-50593 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-11-02 | GSE63130 | GEO

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq]

2015-11-02 | GSE68282 | GEO

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P21]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 21 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 105 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~50 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

2015-11-02 | GSE68284 | GEO

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P30]

2015-11-02 | GSE68283 | GEO