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Genome-wide analyses of Su(Hw) binding in Drosophila ovary

ABSTRACT: The twelve zinc finger Suppressor of Hairy-wing [Su(Hw)] protein binds thousands of sites in Drosophila genome and is essential for the function of the gypsy insulator. Loss of the globally expressed Su(Hw) protein causes female sterility due to tissue-specific defect limited to female germline. Using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq), we determine the extent of tissue-specific binding of Su(Hw) in Drosophila ovary. We demonstrate that Su(Hw) binding sites (SBSs) are largely constitutively occupied in the germline and soma. Our analyses indicate that SBSs fall into several non-uniform classes, as determined by the partner protein distribution and DNA sequence conservation. Further, we show that only a subset of SBSs is required for the female fertility. These sites are maintained in the su(Hw)f zinc finger 10 mutant background, which is fertile but does not support gypsy insulator function. Together, our data are consistent with the model where Su(Hw) serves multiple regulatory roles in the genome, and contribute to understanding of how loss of a single zinc finger affects chromosome localization of a DNA binding protein.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE33052 | GEO | 2011/10/19

SECONDARY ACCESSION(S): PRJNA149457

REPOSITORIES: GEO

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Genome-wide analyses of Su(Hw) binding in Drosophila ovary

Project description:The twelve zinc finger Suppressor of Hairy-wing [Su(Hw)] protein binds thousands of sites in Drosophila genome and is essential for the function of the gypsy insulator. Loss of the globally expressed Su(Hw) protein causes female sterility due to tissue-specific defect limited to female germline. Using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq), we determine the extent of tissue-specific binding of Su(Hw) in Drosophila ovary. We demonstrate that Su(Hw) binding sites (SBSs) are largely constitutively occupied in the germline and soma. Our analyses indicate that SBSs fall into several non-uniform classes, as determined by the partner protein distribution and DNA sequence conservation. Further, we show that only a subset of SBSs is required for the female fertility. These sites are maintained in the su(Hw)f zinc finger 10 mutant background, which is fertile but does not support gypsy insulator function. Together, our data are consistent with the model where Su(Hw) serves multiple regulatory roles in the genome, and contribute to understanding of how loss of a single zinc finger affects chromosome localization of a DNA binding protein. Examination of Su(Hw) localization in the ovaries of less than 6 hour old wild type and su(Hw)f mutant Drosophila females

2011-10-19 | E-GEOD-33052 | biostudies-arrayexpress

Expression analyses in Drosophila ovaries

2013-03-20 | GSE45286 | GEO

Expression analyses in Drosophila ovaries

Project description:Suppressor of Hairy-wing [Su(Hw)] is a multi-zinc finger DNA binding factor required for gypsy insulator function and female germline development in Drosophila. The enhancer-blocking and barrier functions of the gypsy retrotransposon involve Su(Hw) binding to twelve clustered Su(Hw) binding sites (SBSs) and recruitment of the Centrosomal Protein of 190 kD (CP190) and Modifier of mdg4 67.2 kD isoform (Mod67.2) insulator proteins. In contrast, the Su(Hw) germline function involves binding to non-clustered genomic SBSs and does not require CP190 or Mod67.2. Here, we use genome-wide expression analyses in the ovary to identify the first Su(Hw) regulated target genes. Ovaries for RNA isolation were dissected from 4-6 hour old virgin females of wild type (Canton S and BL15598) and su(Hw) null sterile mutants (su(Hw)A2663/v and su(Hw)Pb/2) Drosophila melanogaster. At this stage of development, ovaries only contain egg chamber stages 1-8. Loss of Su(Hw) causes apoptosis at stage 9. Thus, the experimental design compares transcriptional changes in the ovary prior to induction nof apoptosis in su(Hw) mutants.

2013-03-20 | E-GEOD-45286 | biostudies-arrayexpress

in vivo binding of su(Hw) in the Drosophila genome

Project description:There is considerable evidence that insulator elements are likely to play a key role in the organisation of the regulatory architecture of the genome. In Drosophila, one of the best studied insulator elements is the gypsy insulator in the gypsy retrotransposon whose function is dependent on the Su(Hw) Zn-finger DNA binding protein. Although there are several hundred Su(Hw) sites in the genome which are proposed to act as endogenous insulator elements, analysis of the role of the Su(Hw) protein has focussed on the gypsy insulator and few endogenous sites have yet been identified. We have used chromatin immunopurification coupled to genomic microarray analysis to identify Su(Hw) binding sites within a representative region of the Drosophila genome; the 3MB Adh region on chromosome 2L. We have located about 60 Su(Hw) binding sites across this region and this has enabled us to construct a robust new Su(Hw) binding site consensus based on these in vivo sites. In contrast to the gypsy insulator which contains 12 Su(Hw) binding sites within 340bp, the endogenous sites are not present in clusters. We identify two key features of these endogenous Su(Hw) sites. Firstly, in contrast to most analyses of DNA binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Secondly, examination of Su(Hw) binding site occupancy in 0-20hr embryos, 3rd larval instar brains or 3rd larval imaginal discs reveals a constant pattern of Su(Hw) binding indicating that most , if not all Su(Hw) sites are constitutively occupied. These two features support a constant genomic architectural role for the Su(Hw) protein. Keywords: ChIP-chip

2006-06-20 | GSE4691 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Project description:Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and their normal localization is correlated with proper insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) are also required for recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy binding site DNA, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.

2022-10-14 | PXD032165 | Pride

Genome wide analyses of Su(Hw)M393 binding in the Drosophila ovary

Project description:The Suppressor of Hairy-wing [Su(Hw)] protein is a twelve zinc-finger DNA binding transcriptional regulator. Here, we map the genome wide association of Su(Hw) protein expressed from the novel su(Hw)M393 allele, which encodes a protein with a C350S substitution that inactivates ZF4. These analyses demonstrate that ZF4 is required for association with a subset of Su(Hw) binding sites and suggests that these sites may be primarily associated with insulator function.

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Gene expression analyses from 3-day testes of D. melanogaster

Project description:Suppressor of Hairy-wing [Su(Hw)] is a globally expressed twelve-zinc finger transcription factor in Drosophila. Su(Hw) is well-known for its role in establishing the gypsy insulator within the gypsy retrotransposon. A direct role of Su(Hw) in gene activation and repression was uncovered through the study in the Drosophila oogenesis, revealing that Su(Hw)-dependent repression of neuronal genes is essential for egg production. Motivated from the spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis. We discovered that Su(Hw) is required for sperm development and male fertility. Data presented here examined the transcriptional role of Su(Hw) in the Drosophila testis. These studies identified ~400 genes with altered expression in the absence of Su(Hw). Coupled with whole-genome Su(Hw) binding profiles, we identified 145 direct targets of Su(Hw) regulation, of which ~80% show increased transcription upon Su(Hw) loss. Upregulated Su(Hw) targets are enriched for neuronal expression, emphasizing that Su(Hw) represents a functional homolog of mammalian REST that represses neuronal gene expression in non-neuronal tissues.

2018-01-25 | GSE109601 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

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Isha is a su(Hw) mRNA-binding protein required for insulator function [RIP-seq]

Project description:Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here we utilized RNA-affinity pull down coupled with mass spectrometry to identify a novel RNA-binding protein, Isha, that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif (RRM) and RNA Polymerase II CTD-interacting domain (CID). We found that Isha physically interacts with total and elongating RNA Pol II and associates with chromatin at the 5’ end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with gypsy factor CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.

2022-05-26 | GSE200994 | GEO

Isha is a su(Hw) mRNA-binding protein required for insulator function [ChIP-seq]

2022-05-26 | GSE200993 | GEO