Background: SWI/SNF chromatin remodeling complexes consist of many subunits that are combined combinatorially to define distinct forms of the remodeling complex. The AT-rich DNA binding domain containing subunits, ARID1A and ARID2 are two such defining subunits of the BAF and PBAF forms of SWI/SNF. The ARID subunits are highly mutated in a wide variety of cancers, with mutations being particularly common in hepatocellular carcinoma. ARID1A and ARID2 mutations are mutually exclusive, and the pattern of mutations in these subunits suggest they function as tumor suppressors in the same pathway. However, the precise mechanism of action, the transcriptional programs these subunits control, and the interaction between different forms of the SWI/SNF complex remain unknown.
Approach: We explored the effect of ARID1A and ARID2 on the transcriptome using RNAseq following knockdown of each complex in a hepatocellular carcinoma cell line. These data sets were integrated with public ChIP-seq data from the same cell line to identify the functional modules in which ARID1A and ARID2 participate. Comparisons between the genes altered in response to loss of ARID1A and ARID2 and the transcriptional regulators associated with these gene sets allowed us to identify several novel factors that functionally interact with SWI/SNF.
Results: Knockdown of each subunit primarily led to distinct changes in the transcriptome of the cell at several expected categories, including cell cycle regulators and DNA damage response genes. Surprisingly, a significant number of genes were changed in both conditions, often in opposing directions, suggesting that ARID1A and ARID2 may functionally antagonize one another at particular targets of genes. Gene set enrichment analysis suggested that opposite-regulated genes are enriched for targets of the histone lysine demethylase PHF8. Computational analysis of public ChIP-seq data and co-immunoprecipitation experiments identified PHF8 as a direct interacting partner of the SWI/SNF complex.
These results suggest that distinct forms of SWI/SNF control separate transcriptional programs. In cases where a gene changes in both knockdown condtions, different forms of the complex often act in opposition to one another. Future examination of the areas of cooperativity and competition between ARID1A and ARID2 will shed light on their role in chromatin state in the liver and hepatocellular carcinoma. Comparison of transcriptional changes after removal of a complex member to public chromatin regulator binding profiles can provide novel insight into the different interactions and the mechanisms of regulation coordinated by distinct forms of the SWI/SNF complex.
This abstract is also presented as Poster A40.
Citation Format: Jesse Raab, Terry Magnuson. Comparison of the gene regulatory programs controlled by the mutually exclusive SWI/SNF subunits ARID1A and ARID2. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR13.