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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ChIPseq analysis of MYST5 (cg1894) in Drosophila S2 cells

ABSTRACT: We report here the genome-wide localization of the histone acetyltransferase MYST5 (cg1984) in Drosophila. ChIP-seq analysis was performed with two anti-MYST5 antibodies in S2 cells. We found MYST5 to bind to the promoters of actively transcribed genes. MYST5 furthermore showed extensive colocalization with boundary/ insulator factors, including Chriz/ Chromator, CP190, dCTCF and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains. Examination of genome-wide MYST5 localization in S2 cells

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Ann Ehrenhofer-Murray

PROVIDER: E-GEOD-66212 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes.

Heseding Christiane C Saumweber Harald H Rathke Christina C Ehrenhofer-Murray Ann E AE

Chromosoma 20160219 1

MYST family histone acetyltransferases play important roles in gene regulation. Here, we have characterized the Drosophila MYST histone acetyltransferase (HAT) encoded by cg1894, whose closest homolog is Drosophila MOF, and which we have termed MYST5. We found it localized to a large number of interbands as well as to the telomeres of polytene chromosomes, and it showed strong colocalization with the interband protein Z4/Putzig and RNA polymerase II. Accordingly, genome-wide location analysis by ...[more]

PMID: 26894919

Similar Datasets

ChIPseq analysis of MYST5 (cg1894) in Drosophila S2 cells

Project description:We report here the genome-wide localization of the histone acetyltransferase MYST5 (cg1984) in Drosophila. ChIP-seq analysis was performed with two anti-MYST5 antibodies in S2 cells. We found MYST5 to bind to the promoters of actively transcribed genes. MYST5 furthermore showed extensive colocalization with boundary/ insulator factors, including Chriz/ Chromator, CP190, dCTCF and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains.

2016-02-23 | GSE66212 | GEO

Illumina Sequencing data of the influence on gene expression of insulator protein co-factor dMes-4

Project description:The Drosophila insulator-binding proteins (IBPs) dCTCF/Beaf32 mark the physical borders of chromosomal domains involving co-factors that participate in long-range interactions. Chromosomal borders are further enriched in specific histone modifications yet the implication of histone modifiers and nucleosome dynamics remains largely unknown in such context. Here, we show that IBP depletion impairs nucleosome dynamics over genes flanked by their binding sites. Biochemical purification identifies a key histone methyltransferase of H3K36, NSD/dMes-4, as a novel co-factor of IBPs involved in chromatin accessibility, which specifically co-regulates hundreds of genes flanked by Beaf32/dCTCF. dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-mediated H3K36me3, RNA splicing and nucleosome positioning. Our results unveil a model for how IBPs regulate gene expression and nucleosome dynamics through NSD/dMes-4, which may contribute to regulate H3K27me3 spreading. Together, our data suggest a division of labor for how IBPs may dynamically regulate chromatin organization depending on distinct co-factors. mRNA profiles of Beaf32-depleted or Wild-Type control Drosophila S2 cells by RNASeq (Illumina)

2014-04-30 | E-GEOD-57167 | biostudies-arrayexpress

Illumina Sequencing data of Insulator Proteins and the co-factor dMes-4

Project description:The Drosophila insulator-binding proteins (IBPs) dCTCF/Beaf32 mark the physical borders of chromosomal domains involving co-factors that participate in long-range interactions. Chromosomal borders are further enriched in specific histone modifications yet the implication of histone modifiers and nucleosome dynamics remains largely unknown in such context. Here, we show that IBP depletion impairs nucleosome dynamics over genes flanked by their binding sites. Biochemical purification identifies a key histone methyltransferase of H3K36, NSD/dMes-4, as a novel co-factor of IBPs involved in chromatin accessibility, which specifically co-regulates hundreds of genes flanked by Beaf32/dCTCF. dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-mediated H3K36me3, RNA splicing and nucleosome positioning. Our results unveil a model for how IBPs regulate gene expression and nucleosome dynamics through NSD/dMes-4, which may contribute to regulate H3K27me3 spreading. Together, our data suggest a division of labor for how IBPs may dynamically regulate chromatin organization depending on distinct co-factors. ChIP-Seq profiles of H3K36 methylation and RNA Pol II in Drosophila S2 cell line (wild-type) cells

2014-04-30 | E-GEOD-57165 | biostudies-arrayexpress

Distribution of insulator proteins CP190, dCTCF, Su(Hw) and Mod(mdg4)2.2 in Drosophila S2 cells in the presence or absence of dPARP inhibitor 3AB

Project description:We mapped the localization of insulator proteins in Drosophila S2 cells in the presence or absence of 12mM of 3AB. We found that inhibition of PARylation affects DNA binding of insulator proteins only at a small subsets of genomic sites. Examination of genomic occupancy for insulator proteins in S2 cells with or without 3AB inhibition.

2013-09-15 | E-GEOD-41354 | biostudies-arrayexpress

Active chromatin and transcription play a key role in chromosome partitioning into topologiÑ?ally associating domains

Project description:Recent advances enabled by Hi-C technique have unraveled principles of chromosomal folding, which were since linked to many genomic processes. In particular, Hi-C revealed that chromosomes of animals are organized into Topologically Associating Domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. However, mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principals of TAD folding in Drosophila melanogaster, we performed Hi-C and PolyA+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e. the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predict TAD boundaries much worse than the active chromatin marks (in the minimal case, H3K4me3 and total RNA) do. Moreover, inter-TADs correspond to decompacted interbands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin that cannot be organized into compact structures, possibly due to high levels of histone acetylation. Finally, we test this hypothesis by polymer simulations, and find that TAD partitioning can be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin. Hi-C experiments, PolyA+ RNA profiling and mapping of chromosomal rearrangements in four Drosophila melanogaster cell lines.

2015-10-26 | E-GEOD-69013 | biostudies-arrayexpress

Illumina Sequencing data of the influence of Insulator Proteins on chromatin

Project description:The Drosophila insulator-binding proteins (IBPs) dCTCF/Beaf32 mark the physical borders of chromosomal domains involving co-factors that participate in long-range interactions. Chromosomal borders are further enriched in specific histone modifications yet the implication of histone modifiers and nucleosome dynamics remains largely unknown in such context. Here, we show that IBP depletion impairs nucleosome dynamics over genes flanked by their binding sites. Biochemical purification identifies a key histone methyltransferase of H3K36, NSD/dMes-4, as a novel co-factor of IBPs involved in chromatin accessibility, which specifically co-regulates hundreds of genes flanked by Beaf32/dCTCF. dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-mediated H3K36me3, RNA splicing and nucleosome positioning. Our results unveil a model for how IBPs regulate gene expression and nucleosome dynamics through NSD/dMes-4, which may contribute to regulate H3K27me3 spreading. Together, our data suggest a division of labor for how IBPs may dynamically regulate chromatin organization depending on distinct co-factors. Nucleosome profiles of Beaf32-depleted or Wild-Type control Drosophila S2 cells by MNase-Seq (Illumina/TruSeq) for total/bulk nucleosomes or following immunoprecipitation with anti-H3K27me3 antibodies

2014-04-30 | E-GEOD-57166 | biostudies-arrayexpress

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function

Project description:Chromatin insulators and Polycomb group (PcG) complexes control nuclear organization to effect changes in gene expression. In Drosophila, RNA silencing pathways influence long range interactions mediated by PcG proteins and nuclear localization of the gypsy insulator; however, the underlying mechanisms are unknown. Here, we identify a singular requirement for Argonaute2 (AGO2) for the activity of the CCCTC-binding factor (CTCF)/Centrosomal protein 190 (CP190) dependent Fab-8 insulator. AGO2 and CP190 interact physically, and genome wide localization of AGO2 by chromatin immunoprecipitation and sequencing (ChIP-seq) reveals extensive colocalization of AGO2 with insulators and Polycomb Response Elements (PREs) but minimal overlap with regions of endogenous small interfering RNA (endo-siRNA) production. Finally, depletion of either CTCF or CP190 results in loss of AGO2 association with insulators, PREs, and other cis-regulatory regions. Our findings suggest that Dicer-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome. ChIP-seq of AGO2 in two Drosophila cell types (S2 and S3)

2011-08-15 | E-GEOD-22623 | biostudies-arrayexpress

Distribution of histone modificiation H3K27me3 in Drosophila Kc cells, comparison with dCTCF knockdown

Project description:Here we map the localization of H3K27me3 in Drosophila Kc cells, as well as in Drosophila Kc cells wherein dCTCF is knock down. examination of genomic occupancy for H3K27me3, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

2012-06-18 | E-GEOD-37444 | biostudies-arrayexpress

Polycomb Group proteins are retained at specific sites on chromatin in mitosis

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.

2013-01-04 | E-GEOD-38166 | biostudies-arrayexpress

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.

2010-05-19 | E-GEOD-15661 | biostudies-arrayexpress

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