ModENCODE_Lieb and White Lab: unltra-deep sequencing data of genomic DNA, chromatin input, and ChIP of Su(Hw) and H3K36me3 from S2 cells on Illumina Genome Analyzer.
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE27679 | GEO | 2011/03/04
REPOSITORIES: GEO
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Project description:This is a dataset generated by the modENCODE Project. It contains both the pair-end and single-end sequencing data of genomic DNA, chromatin input and the ChIP of the factors Su(Hw) and H3K36me3 from Drosophila S2 cells and it was generated on Illumina Genome Analyzer. The goal was to sequence ~120M tags of each sample and used this ultra-deep dataset to systematically evaluate both experimental and computational factors that influence the results of ChIP-seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf S2 cells from the modENCODE batch were amplified before transferring to the plates. 15 plates were put in culture until the cells reached the appropriate concentration. Cells were harvested from 2 plates to extract the genomic DNA. The remaining 13 plates were then treated with formaldehyde at the same time and the chromatin were extracted. 3 plates were used to produce an Input sample corresponding to the chromatin DNA of the treated cells. Each plate corresponding to an eppendorff tube of chromatin, ChIP experiments were performed on 5 tubes for H3K36me3 and on 5 tubes for Su(Hw). ChIP and DNA extraction were performed independently on each tube. After the purification of the DNA, the tubes corresponding to the same sample (Su(Hw), H3K36me3, Input and gDNA) were pooled together. After mixing, each sample was aliquoted again into 5 tubes. 1 aliquot of each was used for ChIP-chip on Affymetrix tiling arrays for quality control, 1 aliquot was used for single-end sequencing at the University of Chicago HGAC, 1 aliquot was used for single-end sequencing at UNC, 1 aliquot was used for paired-end sequencing at UNC and the remaining aliquot was kept as a back-up of the original samples. For each sample, >100M single-end tags were produced (~5 runs), along with the tags from 1 lane of paired-end sequencing experiment. Besides several experimental factors, the performance of multiple peak callers were evaluated at different sequencing depths.
2011-03-04 | E-GEOD-27679 | biostudies-arrayexpress
Project description:We examined the effects of loss of su(Hw) on gene expression in both carefully staged 3rd instar larvae (selected at the soft white pre-pupae stage) and wing imaginal discs from these animals. su(Hw) null animals were generated by crossing su(Hw)v mutants with a deficiency (Df(3R)ED5644), homozygous individuals were recognised be the lack of the dominat Tb marker carried on the TM6B marker. Keywords: ChIP-chip
2007-07-31 | GSE7682 | GEO
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
Project description:Suppressor of Hairy wing (Su(Hw)) is an insulator protein that participates in regulating chromatin architecture and gene repression in Drosophila. In previous studies we have shown that Su(Hw) is also required for pre-replication complex (pre-RC) recruitment on Su(Hw)-bound sites (SBSs) in Drosophila S2 cells and pupa. Here, we describe the effect of Su(Hw) on developmentally regulated amplification of 66D and 7F Drosophila amplicons in follicle cells (DAFCs), widely used as models in replication studies. We show Su(Hw) binding co-localizes with all known DAFCs in Drosophila ovaries, whereas disruption of Su(Hw) binding to 66D and 7F DAFCs causes a two-fold decrease in the amplification of these loci. The complete loss of Su(Hw) binding to chromatin violates pre-RC recruitment to all amplification regulatory regions of 66D and 7F loci at early oogenesis (prior to DAFCs amplification). These changes coincide with a considerable Su(Hw)-dependent condensation of chromatin at 66D and 7F loci. Although we observed the Brm, ISWI, Mi-2, and CHD1 chromatin remodelers at SBSs genome wide, their remodeler activity does not appear to be responsible for chromatin decondensation at the 66D and 7F amplification regulatory regions. We have discovered that, in addition to the CBP/Nejire and Chameau histone acetyltransferases, the Gcn5 acetyltransferase binds to 66D and 7F DAFCs at SBSs and is dependent on Su(Hw). We propose that the main function of Su(Hw) in developmental amplification of 66D and 7F DAFCs is to establish a chromatin structure that is permissive to pre-RC recruitment.
2021-08-22 | GSE168894 | GEO
Project description:Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) IBP to genome topology remains unclear. In this study, we provide evidence for the existence of long-range interactions (LRIs) between Su(Hw) and Combgap ChIP-Seq peaks, reflected in the indirect binding of these proteins to chromatin in ChIP experiments. Loss of Su(Hw) binding results in the disappearance of Su(Hw)-Combgap LRIs and a decrease in spatial self-interactions among a subset of Su(Hw) sites. Our findings suggest that Su(Hw)-Combgap LRIs are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding.
2024-05-24 | GSE231576 | GEO
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.
2017-02-02 | GSE86243 | GEO
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.
2011-10-19 | GSE33052 | GEO
Project description:modENCODE_submission_3718 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. 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-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 6; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG8573_RNAi&oldid=39388
2011-10-12 | E-GEOD-32812 | biostudies-arrayexpress
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
Project description:Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines
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