ChIP-Seq with Kumgang (Kmg), dMi-2, and Aly from wild-type and kmg KD Drosophila melanogaster testes
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE89381 | GEO | 2017/05/18
SECONDARY ACCESSION(S): PRJNA352406
REPOSITORIES: GEO
Similar Datasets
Project description:The effect of different spermatocyte-specific loss of functions; kumgang (kmg or CG5204), dMi-2 in the gene expression in fly testes was assessed by RNA-Seq. Gene expression in wild-type heads were also measured to have a reference expression profile of 'somatic tissues'. / Title: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression / Abstract: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation. Our results suggest that as new regions of the genome become open for transcription during terminal differentiation, blocking the action of a promiscuous activator on cryptic promoters is a critical mechanism for specifying precise gene activation.
2017-05-18 | GSE89380 | GEO
Project description:The effect of different loss of functions; kumgang (kmg or CG5204), dMi-2, and kmg and always early (aly) double on the gene expression in spermatocyte differentation was assessed by microarray. TITLE: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression ABSTRACT: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation. Our results suggest that as new regions of the genome become open for transcription during terminal differentiation, blocking the action of a promiscuous activator on cryptic promoters is a critical mechanism for specifying precise gene activation.
2017-05-18 | GSE68696 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Abstract To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation. Our results suggest that as new regions of the genome become open for transcription during terminal differentiation, blocking the action of a promiscuous activator on cryptic promoters is a critical mechanism for specifying precise gene activation.
2017-05-18 | GSE89506 | GEO
Project description:Drosophila melanogaster males mutant for any meiotic arrest gene have defective spermatogenesis, with cells arresting as primary spermatocytes, and failing to progress to later stages. This phenotype is remarkably similar to meiosis I maturation arrest azoospemia in humans. Drosophila meiotic arrest genes can be categorised as "aly-class" or "can-class". The aly-class (aly, zaa and zab) regulates both meiotic division and male germ line differentiation by controlling transcriptional activation of a large set of target genes in primary spermatocytes. This set includes genes required for cell cycle progression and those required for spermatid differentiation. The can-class control transcription of the same set of differentiation genes, but not cell cycle genes. aly belongs to a protein family conserved from humans to plants. Aly protein locates to chromatin in wild type individuals, and probably controls transcriptional activity of target promoters through interaction with a DNA binding protein. Objectives: So far aly- and can-class target genes have been identified by the small-scale approach of individually testing cDNA clones (total 18). Expression of 7 genes was unaffected by the mutations (group A), transcription of 8 depended on both classes of genes (group B), finally three genes required the aly- but not the can-class for their expression (group C). The aly-class targets (group C) are particularly intriguing, since they include a gene, boule, whose human homologue deleted in azoospermia (DAZ) is essential for male fertility. This project will address the following questions: How many genes in total are regulated by the meiotic arrest genes? What types of proteins do they encode? Are they all testis specific, or are they expressed at other stages of the life cycle? What is their relevance for fertility in other species?<br> <br> Plan: We will prepare samples of wild type, aly, can, zaa and zab testes. Those transcripts expressed in wild type testes will be placed into group A, B or C based on analysis of the competitive hybridisation of wild type samples vs each mutant in turn. Microarrays will also enable us to determine whether there is a group D, consisting of genes whose down-regulation in spermatocytes is dependent on the meiotic arrest genes. We have dissected testes from 0-1 day old males of the relevent genotypes. We estimate to get >20 ug total RNA from 100 flies, so have dissected at least 500 males of each mutant genotype, and 2000 of wild type (red e, the background chromosome for aly and can). In total we have about 5000 flies worth of testes in the freezer. We have been careful to only include testes and seminal vesicles, and have excluded other tissues from the genital tract. All the males are collected from bottles that are emptied daily, to ensure they are all the same age. Because of their age relatively few of the males will have mated. For aly and can we have used well characterised null alleles. For zab we have used the only mutant allele, which we also know is a null. We havn't cloned zaa so have no idea whether the only existing mutant allele is null. The testes were dissected in testis buffer over a period of 30 min. Then they were transfered into a very small drop of testis buffer in an eppendorf and frozen in liquid nitrogen. They have been stored at -80C. Before being sent to Cambridge we will defrost the samples, add trizol, and pool samples to supply 3 or 4 tubes per genotype.
2004-05-07 | E-FLYC-5 | biostudies-arrayexpress
Project description:Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression
| PRJNA352401 | ENA
Project description:Transposable elements act as promiscuous cryptic promoters that upregulate oncogenes (“onco-exaptation”) in many cancers.
2019-02-05 | GSE113946 | GEO
Project description:modENCODE_submission_3382 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: aly-2; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene aly-2; Strain OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29481 | biostudies-arrayexpress
Project description:modENCODE_submission_3384 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: aly-2; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene aly-2; Strain OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29482 | biostudies-arrayexpress
Project description:modENCODE_submission_3383 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: L2; Genotype: unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene aly-2; Strain OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius
2013-02-04 | E-GEOD-44006 | biostudies-arrayexpress
Project description:The expression of a very large number of genes changes as male germ cells pass through differentiation into spermatids and then sperm. Much of this transcriptional programme requires the activity of the meiotic arrest genes. We extracted RNA from wild type testes, as well as aly mutants and Nxt1 mutants, and used microarrays to compare gene expression profiles. We dissected testes from 0-1 day old Drosophila males, taking care to remove accessory glands and ejaculatory ducts. The control sample expressed a tin-RNAi construct, and had normal testes. The aly mutant were homozygous for aly[5]. The Nxt1 mutants were Nxt1[z2-0488]/Nxt1[DG05102].
2013-06-27 | E-GEOD-48312 | biostudies-arrayexpress