Genome binding/occupancy profiling by high throughput sequencing
Summary
Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely unknown. Here, we comprehensively map complex assemblies on chromatin and find that ncBAF uniquely localizes to CTCF sites and promoters. We identified ncBAF subunits as major synthetic lethalities specific to human synovial sarcoma and malignant rhabdoid tumor, which share in common cBAF complex perturbation. Chemical degradation of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes retain their hallmark localization to CTCF sites and promoters, and maintain gene expression at retained mSWI/SNF sites to support cell proliferation in a manner distinct from fusion oncoprotein-mediated targeting. Taken together, these findings unmask the unique targeting and function of ncBAF complexes and present new cancer-specific therapeutic targets.
Overall design
Genomic profiling of mSWI/SNF complex subtypes in naïve EoL-1 and MOLM-13 by ChIP-seq for complex-specific subunits and histone marks, as well as ChIP-seq for BRD9 subunit in nairve Jurkat cellls. SYO-1 cells were lentivirally infected with vectors containing either shControl or shSSX to assess BRD9 complex localization in synovial sarcoma disease setting. BRD9 ChIP was performed in TTC1240 after lentiviral infection with empty vector control or SMARCB1 to assess BRD9 localization in malignant rhaboid tumor.
To assess SMARCA4 loss upon dBRD9 treatment in MOLM13, cells were treated with 250nM dBRD9 (at a 1:10,000 dilution) or DMSO control for 6 days and then used for ChIP-seq with a SMARCA4 antibody. To examine BRD9 localization in Aska, cells were lentivirally infected with pLKO shScramble or shSSX1 and fixed for ChIP 7 days post infection. In TTC1240, CTCF ChIP was performed on cells lentivirally infected with an empty vector to compare to BRD9 localization before and after SMARCB1 reintroduction in the same cell line. To assess residual complex localization in TTC1240 upon BRD9 loss, BRD9 and SMARCA4 ChIP-seq was performed in TTC1240 cells treated with either 250nM dBRD9 (1:10,000 dilution) or DMSO control for 7 days. ChIPs were spiked in for normalization and SMARCA4 ChIP was performed in duplicate from independent samples.
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