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The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

ABSTRACT: Background: The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results: Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread colocalization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions: Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE36450 | GEO | 2013/02/06

SECONDARY ACCESSION(S): PRJNA153201

REPOSITORIES: GEO

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The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

Project description:Background: The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results: Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread colocalization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions: Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes. Refer to individual Series

2013-02-06 | E-GEOD-36450 | biostudies-arrayexpress

Chromatin maps of the Drosophila melanogaster TrxG protein Ash1 and FSH

Project description:Trithorax group (TrxG) proteins counteract Polycomb silencing by an as yet uncharacterized mechanism. A well-known member of the TrxG is the histone methyltransferase Absent, Small, or Homeotic discs 1 (ASH1). In Drosophila ASH1 is needed for the maintenance of Hox gene expression throughout development, which is tightly coupled to preservation of cell identity. In order to understand the molecular function of ASH1 in this process, we performed affinity purification of tandem-tagged ASH1 followed by mass spectrometry (AP-MS) and identified FSH, another member of the TrxG as interaction partner. Here we provide genome-wide chromatin maps of both proteins based on ChIP-seq. Our Dataset comprises of 4 ChIP-seq samples using chromatin from S2 cells which was immunoprecipitated, using antibodies against Ash1, FSH-L and FSH-SL.

2013-06-30 | E-GEOD-30820 | biostudies-arrayexpress

Chromatin maps of the Drosophila melanogaster TrxG protein Ash1 and FSH

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A Polycomb Repressive Complex 1 proteome from Drosophila cells

Project description:Polycomb Group (PcG) proteins regulate gene expression through changes to chromatin structure and are essential for development. PcG proteins function together with the Trithorax Group (TrxG) proteins, which affect diverse steps in transcription activation. The PcG and TrxG are genetically and functionally antagonistic, and current understanding suggests a balance of their activities can maintain a wide range of transcription states. PcG and TrxG proteins assemble into a series of complexes. How these complexes work together, how PcG complexes are recruited to target genes, and whether other proteins are involved in their regulation of gene expression remain open questions. We carried out tandem affinity purification followed by mass spectrometry (TAP-MS) on two core components of Drosophila Polycomb Repressive Complex 1 (PRC1). Our data reveal a network of interactions among PcG complexes, and extensive co-purification of TrxG complexes with PRC1. We co-purified >50 transcription factors with PRC1 that were not previously linked to the PcG. Finally, we identify novel co-purifying complexes, including HP1c and PCNA handling complexes. Our resource of candidate PRC1 interacting proteins generate new hypotheses for PRC1 function.

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Distribution of TrxG, RNA Pol II and associated histone marks in Sg4 cells

Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac, H3K9ac in cultured Drosophila Sg4 cells by hybridization of ChIP products with tiling microarrays.

2010-01-08 | GSE18176 | GEO

Distribution of PcG, TrxG, RNA Pol II and associated histone marks in ML-DmD23-c4 cells

Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmD23-c4 cells by hybridization of ChIP products with tiling microarrays

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Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmBG3-c2 cells by hybridization of ChIP products with tiling microarrays.

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Ash1 ChIP-chip data from murine Embyonic Stem cells

Project description:Ash1 is a Trithorax Group (TrxG) protein with histone methyl transferase activity that is associated with gene activation. Here we use ChIP-chip to determine the occupancy of Ash1 at promoters in murine embryonic stem cells. This dataset includes singlet ChIP-chip data targeting Ash1 in murine Embryonic stem cells.

2010-05-14 | E-GEOD-20063 | biostudies-arrayexpress

Polycomb preferentially targets stalled promoters of coding and non-coding transcripts

Project description:The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study, we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition to finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG-binding sites coinciding with non-annotated transcription start sites. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to non-coding RNAs essential for development, apoptosis and growth.

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