Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

ABSTRACT: Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of CP190 in stably transfected Drosophila S2 cell lines expressing in Wild-Type Beaf (Control) or Mutant Beaf by ChIP-Seq (Illumina)

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Olivier Cuvier

PROVIDER: E-GEOD-52886 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of Beaf-32 in Drosophila S2 cells by ChIP-Seq (Illumina)

2014-02-01 | E-GEOD-52962 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [RNA-Seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify M-bM-^@M-^Xindirect peaksM-bM-^@M-^Y of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. mRNA profiles of stably transfected Drosophila S2 cell lines expressing Wild-Type or Mutant Beaf by RNASeq (Illumina/TruSeq), in triplicates

2014-02-01 | E-GEOD-52884 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

2014-02-01 | GSE52962 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

2014-02-01 | GSE52886 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [RNA-Seq]

2014-02-01 | GSE52884 | GEO

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Project description:Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) IBP to genome topology remains unclear. In this study, we provide evidence for the existence of long-range interactions (LRIs) between Su(Hw) and Combgap ChIP-Seq peaks, reflected in the indirect binding of these proteins to chromatin in ChIP experiments. Loss of Su(Hw) binding results in the disappearance of Su(Hw)-Combgap LRIs and a decrease in spatial self-interactions among a subset of Su(Hw) sites. Our findings suggest that Su(Hw)-Combgap LRIs are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding.

2024-05-24 | GSE231576 | GEO

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [ChIP_seq_S2]

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 | GSE169408 | GEO

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

2022-07-14 | GSE169407 | GEO

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_S2]

2022-07-14 | GSE169413 | GEO

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

2022-07-14 | GSE169412 | GEO