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Mapping genomic loci bound to BRD2 in Calu-3 cells

ABSTRACT: Mapping genomic loci bound to BRD2 in Calu-3 cells

PROVIDER: PRJNA692840 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13453746_1.fastq.gz	Fastqsanger.gz
	SRR13453746_2.fastq.gz	Fastqsanger.gz
	SRR13453747_1.fastq.gz	Fastqsanger.gz
	SRR13453747_2.fastq.gz	Fastqsanger.gz
	SRR13453748_1.fastq.gz	Fastqsanger.gz

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Mapping genomic loci bound to BRD2 in Calu-3 cells

Project description:we performed CUT&RUN to comprehensively map genomic loci bound to BRD2 in Calu-3 cells. We also included H3K4me3 and IgG antibodies as postive and negative controls, repectively

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BRD2 CUT & RUN in Calu-3 cells

Project description:we performed CUT&RUN to comprehensively map genomic loci bound to BRD2 in control and BRD2 knockdown Calu-3 cells. We also included H2A.Z, H3K4me3 and IgG antibodies.

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BRD2 CUT & RUN in Calu-3 cells

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BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

Project description:We performed RNA sequencing of Calu-3 cells after treatment with the BET-domain inhibitors JQ-1 and ABBV-744 as well as BRD2 CRISPRi knockdown. We also included CRISPRi knockdown of two other validated hit genes from our screen, COMP and ACE2.

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Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data)

Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states. Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.

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The BET protein BRD2 cooperates with CTCF to enforce a transcriptional boundary

Project description:Role of the bromodomain and extraterminal motif (BET) protein BRD2 in CTCF chromatin occupancy, tested by CRISPR/Cas9-mediated depletion of BRD2 in GATA1-null erythroblasts expressing an inducible GATA1-ER fusion (G1E-ER4). Pharmacologic inhibitors of the BET (bromodomain and extraterminal motif) family of proteins are being explored for the treatment of various diseases, including cancer, yet the individual functions of BET proteins remain unclear. Here we find that BRD2 co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Genome editing at a CTCF/BRD2 co-occupied site reveals a functional boundary element that upon perturbation results in transcriptional misregulation. Single-molecule RNA FISH reveals that either site-specific CTCF loss or BRD2 depletion increases the correlation in expression of two genes flanking the boundary. Together these findings indicate that BRD2 supports chromatin boundary activity in a CTCF-dependent manner and suggest that pharmacologic BET inhibitors influence gene expression in part by perturbing chromatin domain boundary function.

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