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Chromatin immunoprecipitation of Drosophila embryos at 6-8h AEL to identify Beaf-32, CP190, CTCF and SuHw proteins binding

ABSTRACT: Chromatin immunoprecipitation of Drosophila embryos at 6-8h AEL to identify Beaf-32, CP190, CTCF and SuHw proteins binding

PROVIDER: PRJEB38618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4183650_1.fastq.gz	Fastqsanger.gz
	ERR4183650_2.fastq.gz	Fastqsanger.gz
	ERR4183651_1.fastq.gz	Fastqsanger.gz
	ERR4183651_2.fastq.gz	Fastqsanger.gz
	ERR4183652_1.fastq.gz	Fastqsanger.gz

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Chromatin immunoprecipitation of Drosophila embryos at 6-8h AEL to identify Beaf-32, CP190, CTCF and SuHw proteins binding

Project description:ChIP-seq against Beaf-32, CP190 or CTCF was performed in wild-type embryos collected between 6 and 8h after egg laying. For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated.

2023-10-31 | E-MTAB-9157 | biostudies-arrayexpress

Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

Project description:Hi-C was performed using the Bridge Adaptor Protocol in 2 biological replicates of Drosophila embryos at NC14 depleted of the maternal deposition of Beaf-32, CP190 or CTCF mRNA and protein. Embryos were collected at 2-3h AEL and were derived from mothers expressing RNAi against Beaf-32 or CP190 in the germline, or were genetic null for the maternal and zygotic contribution of CTCF.

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Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

Project description:Profiling of genes expression changes caused by the depletion of either Beaf-32, CP190 or CTCF during early embryogenesis. Gene expression changes were profiled in embryos at NC14 (manually-selected). Beaf-32 and CP190 were depleted using RNAi and CTCF by using maternal/zygotic null embryos. Poly(A) mRNA-seq was performed from three biological replicates.

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Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify Beaf-32, CP190 and CTCF proteins binding

Project description:Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify Beaf-32, CP190 and CTCF proteins binding

| PRJEB38466 | ENA

Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify binding sites of Beaf-32, CP190, CTCF, Su(Hw) and GAF insulator proteins

Project description:ChIP-seq against Beaf-32, CP190, CTCF, Su(Hw) and GAF was performed in wild-type embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated. Sequencing was performed on Illumina NextSeq 500.

2022-12-17 | E-MTAB-9156 | biostudies-arrayexpress

CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

Project description:CUTnTag against Beaf-32, CP190 and CTCF was performed in wild-type and insulator-depleted embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). Spike-ins from D. virilis were used in each reaction. For each sample, 50k nuclei from each species were mixed together at the start of the protocol. For each protein, CUTnTag was done in biological duplicates. Sequencing was performed on Illumina NextSeq 500.

2022-12-17 | E-MTAB-11993 | biostudies-arrayexpress

Chromatin immunoprecipitation of BEAF-32A and BEAF-32B in Drosophila embryos

Project description:ChIP-chip analysis of BEAF binding sites in Drosophila embryos using three antibodies: one that recognize both BEAF-32A and BEAF-32B, one specific for BEAF-32A and one specific for BEAF-32B

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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)

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Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

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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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