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PBRM1 bromodomains associate with RNA to facilitate chromatin association (CLIP-seq)

ABSTRACT: PBRM1 bromodomains associate with RNA to facilitate chromatin association (CLIP-seq)

PROVIDER: PRJNA915087 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22869203_1.fastq.gz	Fastqsanger.gz
	SRR22869203_2.fastq.gz	Fastqsanger.gz
	SRR22869204_1.fastq.gz	Fastqsanger.gz
	SRR22869204_2.fastq.gz	Fastqsanger.gz
	SRR22869205_1.fastq.gz	Fastqsanger.gz

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PBRM1 bromodomains associate with RNA to facilitate chromatin association (CLIP-seq)

Project description:PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Using H3K14Ac and PHF10 ChIP-seq, along with CLIP-seq in Caki2 renal cancer cells, we demonstrate here that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

2023-02-24 | GSE221619 | GEO

PBRM1 bromodomains associate with RNA to facilitate chromatin association

Project description:PBRM1 bromodomains associate with RNA to facilitate chromatin association

| PRJNA915086 | ENA

PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)

2023-02-24 | GSE221618 | GEO

PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)

Project description:PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)

| PRJNA915088 | ENA

PBRM1 bromodomains associate with RNA to facilitate chromatin association.

Project description:PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here, we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

| S-EPMC10164552 | biostudies-literature

PBRM1 bromodomains associate with RNA to facilitate chromatin association

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-02-24 | GSE221620 | GEO

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci

Project description:This SuperSeries is composed of the following subset Series: GSE25597: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (ChIP-chip) GSE25598: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (expression) GSE25600: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (MNase) Refer to individual Series

2011-01-07 | E-GEOD-25605 | biostudies-arrayexpress

PBRM1 Knockdown in RCC Cell Lines

Project description:PBRM1 was found to be mutated in a high percentage of clear cell RCCs. We performed knockdown of PBRM1 via siRNA and compared with scrambled control in three different RCC cell lines. PBRM1 siRNA and mock treated cell lines were normalized together with 'hypoxic' clear cell renal tumors and normal renal tissue samples from GSE17818.

2011-01-20 | E-GEOD-22316 | biostudies-arrayexpress

PBRM1 deficiency is synthetic lethal with PARP inhibitors in human cancers

Project description:Polybromo-1 (PBRM1), which encodes a specific subunit of the pBAF chromatin remodeling complex, is inactivated in multiple malignancies including 50% of clear cell renal cell carcinoma. At present, a therapeutic strategy that selectively targets PBRM1 defects does not exist. PBRM1 is involved in multiple cellular processes including transcription, replication and DNA repair. Using high-throughput screens and multiple isogenic and non-isogenic models, we found that PBRM1 defects cause synthetic lethality with several clinical PARP inhibitors, both in vitro and in vivo. This effect was enhanced using combinations with either small molecule ATR or BET inhibitors. Mechanistically, PBRM1 defects caused increased replication stress, R-loop formation and genomic instability that was exacerbated by PARP inhibitors. We also found that PARP and ATR inhibitors activate the cGAS-STING innate immunity pathway in PBRM1-deficient but not in PBRM1-proficient cells. These data provide the pre-clinical rationale for assessing PARP inhibitors as a monotherapy or in combination with ATR inhibitors or immune checkpoint inhibitors, in patients with PBRM1-deficient cancers.

2022-02-21 | PXD017826 | Pride

Trancriptomic profiling of HCT116 colon cancer cells with or without PBRM1 knock-down by RNAi

Project description:To investigate the influence of PBRM1 on gene expression, we performed RNA-seq in HCT116 colon cancer cells with or without PBRM1 knock-down by RNAi (both shRNA and siRNA approaches were used), and identified differentially expressed genes in PBRM1 knock-down cells compared to control cells, which shows implications for PBRM1's biological function in colon cancer.

2018-01-30 | E-MTAB-5566 | biostudies-arrayexpress

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