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The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity (ChIP-Seq)

ABSTRACT: Chromatin insulators are DNA-protein complexes that establish distinct higher order transcriptional domains. In Drosophila, CP190 is the only common factor for all the DNA-binding insulator protein complex. Insulators harbour two properties: they can block communication between an enhancer and a promoter, and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy insulator complex contains three core components; Su(Hw), CP190 and Mod(mdg4)67.2. In our studies, using mass-spec analysis and of immunopurified complexes from Drosophila embryonic nuclear extracts, we identified the transcription factor Motif 1 Binding Protein (M1BP) associated with CP190 and verified this interaction by coimmunoprecipitation. Furthermore, depletion of M1BP results in loss of both enhancer-blocking and barrier activities, also disrupts the nuclear localization of CP190-marked insulator bodies within the developing fly. ChIP-seq analysis of both factors in Kc167 cultured hemocytes revealed extensive overlap of the two factors, particularly at Motif 1 containing promoters. Depletion of M1BP results in extensive loss of CP190 chromatin association, and depletion of CP190 also greatly affects M1BP chromatin association. Moreover, EU-seq analysis after depletion of either CP190 or M1BP suggests they regulate gene expression in similar fashion. Further analysis using reporter assays verifies that CP190-dependent gene expression changes are dependent on the presence of Motif 1. Our results suggest a novel mechanistic relationship between CP190 and M1BP function with respect to transcriptional regulation and higher order chromatin organization.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE142531 | GEO | 2020/10/27

REPOSITORIES: GEO

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The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity (RNA-Seq)

Project description:Chromatin insulators are DNA-protein complexes that establish distinct higher order transcriptional domains. In Drosophila, CP190 is the only common factor for all the DNA-binding insulator protein complex. Insulators harbour two properties: they can block communication between an enhancer and a promoter, and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy insulator complex contains three core components; Su(Hw), CP190 and Mod(mdg4)67.2. In our studies, using mass-spec analysis and of immunopurified complexes from Drosophila embryonic nuclear extracts, we identified the transcription factor Motif 1 Binding Protein (M1BP) associated with CP190 and verified this interaction by coimmunoprecipitation. Furthermore, depletion of M1BP results in loss of both enhancer-blocking and barrier activities, also disrupts the nuclear localization of CP190-marked insulator bodies within the developing fly. ChIP-seq analysis of both factors in Kc167 cultured hemocytes revealed extensive overlap of the two factors, particularly at Motif 1 containing promoters. Depletion of M1BP results in extensive loss of CP190 chromatin association, and depletion of CP190 also greatly affects M1BP chromatin association. Moreover, EU-seq analysis after depletion of either CP190 or M1BP suggests they regulate gene expression in similar fashion. Further analysis using reporter assays verifies that CP190-dependent gene expression changes are dependent on the presence of Motif 1. Our results suggest a novel mechanistic relationship between CP190 and M1BP function with respect to transcriptional regulation and higher order chromatin organization.

2020-10-27 | GSE142532 | GEO

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

Project description:Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.

2021-06-07 | PXD026497 | Pride

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity (ATAC-seq)

Project description:Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP is required for CP190 chromatin binding at many shared sites, and CP190 also affects M1BP chromatin association. Both factors are required for Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP alters local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.

2021-04-14 | GSE169105 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Project description:Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and their normal localization is correlated with proper insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) are also required for recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy binding site DNA, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.

2022-10-14 | PXD032165 | Pride

The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: differential ChIP-seq of CP190 and CLAMP under CP190 knockdown

Project description:Chromatin insulators are DNA-protein complexes that establish higher order independent DNA domains to influence transcriptional regulation. Insulators are defined by two different functions: they can block communication between an enhancer and a promoter and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy-insulator complex contains three core components: Su(Hw), CP190 and Mod(mdg4)67.2. Here we identify a novel role for Chromatin-linked adaptor for MSL proteins (CLAMP) in promoting gypsy chromatin insulator function. When Clamp is depleted by RNAi, gypsy-dependent enhancer blocking activity decreases and barrier activity is reduced in all tissues. Furthermore, Clamp RNAi knockdowns and mutation result in disorganized insulator complex localization in the nucleus. Co-immunoprecipitation experiments showed that CLAMP physically associates with core gypsy-insulator proteins. Co-localization of CLAMP with gypsy components on polytene chromosomes and ChIP-seq analysis demonstrates co-localization of CLAMP with a subset of insulator sites across the genome. Thus, our findings suggest a ubiquitous, genome-wide role for CLAMP in promoting gypsy-dependent chromatin insulator activity.

2019-01-28 | GSE118699 | GEO

The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: ChIP-seq of CP190, Su(Hw), Mod(mdg4) for genome-wide overlap with CLAMP

2019-01-28 | GSE103601 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

2022-06-28 | GSE198361 | GEO

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

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

2011-08-15 | GSE22623 | GEO

The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

Project description:Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, improvement of barrier activity is detected only in tissue outside of the central nervous system (CNS) when Rump levels are reduced. Furthermore, rump mutants restore insulator complex localization in an otherwise compromised genetic background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and ChIP-Seq analysis of Rump demonstrates extensive colocalization with a subset of gypsy insulator sites across the genome. The genome-wide binding profile and tissue-specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity exclusively in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity. ChIP-seq of Rump, Mod(mdg4)2.2, Shep, Su(Hw), and CP190 in Drosophila Kc167 cells

2014-04-18 | E-GEOD-51462 | biostudies-arrayexpress

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