Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 1)
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE65566 | GEO | 2016/09/15
SECONDARY ACCESSION(S): PRJNA274378
REPOSITORIES: GEO
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Project description:PcG proteins are critical epigenetic regulators of development. Here we compared genomic distribution of Psc protein in cultured Drosophila cells lacking Su(z)12 protein to that of the wild type.
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Project description:Polycomb group (PcG) proteins are critical epigenetic regulators of development. Here we compared genomic distribution of Polycomb (Pc) protein in cultured Drosophila cells lacking Su(z)12 protein to that of the wild type.
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Project description:Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites. 26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts. PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis.
2013-01-04 | GSE38166 | GEO
Project description:Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites. 26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts. PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis. Drosophila S2 cells were colchicine-treated and stained with anti-H3S10p antibody and FACS sorted to give mitotic samples. In parallel asynchronous Drosophila S2 cell cultures were stained for anti-H3 antibody and FACS sorted to give control samples. Chromatin from each of these sorted populations was immunoprecipitated using biotinylated antibodies against PSC. Two replicates of these samples are included. A stable Drosophila S2 cell line expressing biotin-tagged PH was also FACS sorted as above to give mitotic and control samples, and streptavidin-coated beads were used to pulldown biotinlyated PH. Inputs are included for each sample.
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Project description:To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.
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Project description:To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.
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Project description:To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.
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