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The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [Mnase-seq]

ABSTRACT: The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [Mnase-seq]

PROVIDER: PRJNA811119 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18163692_1.fastq.gz	Fastqsanger.gz
	SRR18163692_2.fastq.gz	Fastqsanger.gz
	SRR18163693_1.fastq.gz	Fastqsanger.gz
	SRR18163693_2.fastq.gz	Fastqsanger.gz
	SRR18163694_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [Mnase-seq]

Project description:We examine the effect of this interaction on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells. We examine the effect of the interaction between BEAF and polybromo on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells.

2022-03-05 | GSE197574 | GEO

The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex

Project description:The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex

| PRJNA811123 | ENA

The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [PRO-seq]

2022-03-05 | GSE197579 | GEO

The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [PRO-seq]

Project description:The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [PRO-seq]

| PRJNA811127 | ENA

The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex.

Project description:The Drosophila Boundary Element-Associated Factor of 32 kDa (BEAF) binds in promoter regions of a few thousand mostly housekeeping genes. BEAF is implicated in both chromatin domain boundary activity and promoter function, although molecular mechanisms remain elusive. Here, we show that BEAF physically interacts with the polybromo subunit (Pbro) of PBAP, a SWI/SNF-class chromatin remodeling complex. BEAF also shows genetic interactions with Pbro and other PBAP subunits. We examine the effect of this interaction on gene expression and chromatin structure using precision run-on sequencing and micrococcal nuclease sequencing after RNAi-mediated knockdown in cultured S2 cells. Our results are consistent with the interaction playing a subtle role in gene activation. Fewer than 5% of BEAF-associated genes were significantly affected after BEAF knockdown. Most were downregulated, accompanied by fill-in of the promoter nucleosome-depleted region and a slight upstream shift of the +1 nucleosome. Pbro knockdown caused downregulation of several hundred genes and showed a correlation with BEAF knockdown but a better correlation with promoter-proximal GAGA factor binding. Micrococcal nuclease sequencing supports that BEAF binds near housekeeping gene promoters while Pbro is more important at regulated genes. Yet there is a similar general but slight reduction of promoter-proximal pausing by RNA polymerase II and increase in nucleosome-depleted region nucleosome occupancy after knockdown of either protein. We discuss the possibility of redundant factors keeping BEAF-associated promoters active and masking the role of interactions between BEAF and the Pbro subunit of PBAP in S2 cells. We identify Facilitates Chromatin Transcription (FACT) and Nucleosome Remodeling Factor (NURF) as candidate redundant factors.

| S-EPMC9635645 | biostudies-literature

BEAF-32 insulator regulates gene expression of genes involved in cell polarity and neoplastic growth.

Project description:This SuperSeries is composed of the following subset Series: GSE36735: Distribution of Drosophila insulator protein BEAF-32 in Wing imaginal tissue (Wildtype) [ChIP-seq] GSE36736: Genome wide transcriptional profiling of BEAF-32 in wing imaginal tissues of wildtype and mutants [expresion array] Refer to individual Series

2012-07-05 | E-GEOD-36737 | biostudies-arrayexpress

Distribution of Drosophila insulator protein BEAF-32 in Wing imaginal tissue (Wildtype) [ChIP-seq]

Project description:Chromatin insulators are DNA protein complexes that mediate inter and intra chromosomal interactions. Boundary Element Associated Factor- 32 (BEAF-32) is an insulator protein predominantly found near gene promoters and thought to play a role in gene expression. We find that mutations in BEAF-32 are lethal, show loss of epithelial morphology in imaginal discs and cause neoplastic growth defects. To investigate the molecular mechanisms underlying this phenotype, we carried out a genome-wide analysis of BEAF-32 localization in wing imaginal disc cells. Mutation of BEAF-32 results in miss-regulation of 3850 genes by at least 1.5-fold, 647 of which are bound by this protein in wing imaginal cells. Up-regulated genes encode proteins such as Bazooka, a determinant of cell polarity; the Insulin receptor-1 and the p70-S6 kinase, involved in the insulin growth factor pathway that can activate various pathways involved in cell proliferation; and the Unpaired 3 ligand of the Janus kinase (JNK) pathway, and its target gene Socs35, which can also activate cell proliferation. The expression of genes involved in DNA homologous end repair and oxidative stress pathways is also increased in BEAF-32 mutants. Among the down-regulated genes are those encoding components of the Wingless pathway, which is required for cell differentiation, and amino acid metabolism. Miss-regulation of these genes explains the unregulated cell growth and neoplastic phenotypes observed in imaginal tissues of BEAF-32 mutants. Here we examine mapping the genomic binding sites and its distribution of BEAF-32, a Drosophila insulator proteins in wing imaginal tissue. We performed ChIP-seq analysis using BEAF-32B.

2012-07-05 | E-GEOD-36735 | biostudies-arrayexpress

Distribution of Drosophila insulator protein BEAF-32 in Wing imaginal tissue (Wildtype) [ChIP-seq]

2012-07-06 | GSE36735 | GEO

ChIP-seq study of BEAF binding in four Drosophila spcies

Project description:Insulators are considered as chromosome organizers. BEAF, one of the insulator proteins, is highly conserved in Drosophila speies but also limited to Drosophila spcies. BEAF associates with TSS of active genes. Comparative study of BEAF binding landscapes in four Drosophila species reveals BEAF association with gene pairs, and the results suggest the role of gain or loss of BEAF binding during the speciation of Drosophila species.

2012-08-03 | GSE35648 | GEO

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_flyheads]

Project description:Chromatin insulators are involved in transcription regulation and long-range chromatin contacts. In Drosophila the Boundary Element-Associated Factor Of 32kD (BEAF-32) binds to promoters of housekeeping genes and the boundaries of Topological Associated Domains (TAD) and is involved in the regulation of long-range targets by mechanisms that remain incompletely understood. Here we show that Relative-Of-WOC (ROW), which is part of the Heterochromatin Protein 1c (HP1c) complex, is essential for the long-range transcription regulation mediated by BEAF-32. We found that ROW physically interacts with the insulator complex proteins BEAF-32 and Chromator, as well as with HP1c, HP1b, and Without Children (WOC). Moreover, we found that ROW binds AT-rich sequences flanked by BEAF-32 motifs, which are located at promoters of housekeeping genes and in TAD boundaries. In agreement with these results, the genome distribution of ROW strongly correlated with BEAF-32 and WOC, but at a lower level with HP1c and HP1b. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32, are indirectly bound by BEAF-32 and ROW, and enriched with factors associated with RNA polymerase II pausing. These results suggest that ROW and BEAF-32 are involved in the recruitment of protein complexes required for transcription activation and long-range contacts between promoters of housekeeping and inducible genes.

2022-07-14 | GSE169412 | GEO

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