Sex comb on midleg (Scm) is a functional link between PcG repressive complexes in Drosophila
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE66183 | GEO | 2015/07/09
SECONDARY ACCESSION(S): PRJNA276074
REPOSITORIES: GEO
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Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing
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Project description:The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGFM-bM-^@M-^SRING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level. ChIP-seq experiments of different PRC1 components were performed either on HA-tagged transgenic stable 293T-REx lines or on endogenous subunits using specific antibodies.
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Project description:The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGF–RING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level.
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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; 5) Micro-C data.
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