BioProject

The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. More...

The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. The SWI/SNF chromatin remodeling complex is made up of multiple subunits that can be filled by mutually exclusive proteins. Inclusion or exclusion of these proteins has profound functional consequences, yet we currently understand little about the direct functional relationship between these biochemically distinct forms of remodeling complexes. Here we combine chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding information from the ENCODE project to determine the functional relationship between three biochemically distinct forms of SWI/SNF. We find widespread overlap in transcriptional regulation and the genomic binding of the three ARID (AT-Rich Interacting Domain) subunits of SWI/SNF. Despite the numerous similarities in their transcriptional regulation and the co-factors bound with each ARID we identify several novel interaction modalities. Previous work has found examples of competition or subunit switching at individual loci, and we find this functional relationship is widespread, and in these cases gene expression changes following loss of one ARID depend on the function of another ARID. We also identify a previously unknown cooperative interaction between ARID1B and ARID2 in the repression of a large number of genes. Together these data help untangle the complicated combinatorial relationships between a highly heterogenous chromatin remodeling family. Overall design: We performed ChIP for 4 subunits of SWI/SNF (Arid1a, Arid1b, Arid2, Snf5) and 2 replicates of each, as well as Input. HepG2 cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees C, then washed and cell pellets were stored at -80 until immunoprecipitation. Nuclei were released using Dounce homogenizer and layered over a sucrose cushion. Chromatin was then prepared by digesting with micrococcal nuclease for 15 minutes at 37 degrees. Chromatin equivalent to 2x10^7 cells was used in each IP with the antibodies listed. All scripts used in the data analysis are available at: http://github.com/jraab/raab_swisnf_2015/ Less...