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SRX18945315: GSM6918839: SMARCA4_786O PBRM1KO_DMSO_24hr_ChIPSeq_rep1; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 43M spots, 12.9G bases, 3.7Gb downloads

External Id: GSM6918839_r1
Submitted by: Genome Institute of Singapore
Study: Genome-wide chromatin profiles of PBRM1 Drug treatment [ChIP-Seq]
show Abstracthide Abstract
PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-?B pathway. PBRM1-deficient PBAF complexes, despite retaining the association between SMARCA4 and ARID2, have loosely tethered BRD7 and redistribute from promoter proximal regions to distal enhancers containing NF-?B motifs. Subsequently, PBRM1-deficient cells display heightened NF-?B activity in multiple models and clinical samples. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib reverses NF-?B activation by reducing RELA occupancy and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-?B target genes by residual PBRM1-deficient PBAF complexes. Overall design: ChIP-seq of parental and PBRM1-deficient 786-O cells treated with SMARCA4 ATPase inhibitor BRM014 and bortezomib
Sample: SMARCA4_786O PBRM1KO_DMSO_24hr_ChIPSeq_rep1
SAMN32602230 • SRS16369326 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6918839
Instrument: Illumina NovaSeq 6000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature. At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on Novaseq
Runs: 1 run, 43M spots, 12.9G bases, 3.7Gb
Run# of Spots# of BasesSizePublished
SRR2298919942,977,85212.9G3.7Gb2023-02-11

ID:
26076828

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