Our objective is to understand how ATP-dependent chromatin remodeling complexes (CRCs) contribute to the regulation of transcription and other vital cellular processes. Chromatin represses transcription, and all eukaryotes utilize a related set of CRCs to remove this repression. The yeast S. cerevisiae contains two related CRCs, SWI/SNF and RSC, which are highly similar in composition and in vitro activities to their metazoan counterparts. Yeast SWI/SNF is a rare, non-essential complex that remodels chromatin at many pol II promoters. In contrast, RSC is both abundant and essential for viability, but its functions are unknown. Human SWI/SNF is both abundant and essential for viability, and mutations can cause aggressive rhabdoid tumors.
Our Specific Aims are to determine how RSC is targeted to particular genomic loci and to identify RSC- interacting proteins, with the goal of understanding more about how these conserved chromatin remodeling complexes contribute to the control of gene expression: 1) Identify the genomic targets for RSC action. The Rsc3 component of RSC is highly similar to known sequence-specific DNA-binding transcriptional activators. We will identify Rsc3 (and RSC) targets through DNA microarray analysis of rsc3 Ts- mutants. The Rsc3 binding site will be determined by site-selection studies, and chromatin immunoprecipitation experiments will be utilized to test candidate promoters for Rsc3 occupancy in vivo. 2) Determine the function of Rsc1, Rsc2, and the bromodomain (BD). Rsc1 and Rsc2 members that contain BDs and a BAH domain, two motifs of unknown function found in many important transcriptional regulators. We will perform a structure/function analysis of the Rsc2 BD using random mutagenesis, isolate conditional mutations, and utilize genetic suppression of conditional mutants to isolate BD- interactions proteins. 3) Examine the structure/function of a BAH region. We will perform a structure/function analysis of the Rsc2 BAH region using random mutagenesis, and utilize suppression of conditional mutants to isolate BAH-interacting proteins. 4) Ascertain the function of actin-related proteins (Arp) in RSC. We will purify RSC lacking Arp proteins and test for function, perform DNA microarray analysis with our arp Ts- mutants, and acquire genetic suppressors of arp mutants to identify cellular processes that require Arp function.
| Clapier, Cedric R; Iwasa, Janet; Cairns, Bradley R et al. (2017) Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 18:407-422 |
| Clapier, Cedric R; Kasten, Margaret M; Parnell, Timothy J et al. (2016) Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Mol Cell 62:453-461 |
| Parnell, Timothy J; Schlichter, Alisha; Wilson, Boris G et al. (2015) The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. Elife 4:e06073 |
| Schubert, Heidi L; Wittmeyer, Jacqueline; Kasten, Margaret M et al. (2013) Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A 110:3345-50 |
| Clapier, Cedric R; Cairns, Bradley R (2012) Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492:280-4 |
| Sirinakis, George; Clapier, Cedric R; Gao, Ying et al. (2011) The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J 30:2364-72 |
| Malik, Shuja Shafi; Rich, Evan; Viswanathan, Ramya et al. (2011) Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC. Biochemistry 50:7881-90 |
| Kasten, Margaret M; Clapier, Cedric R; Cairns, Bradley R (2011) SnapShot: Chromatin remodeling: SWI/SNF. Cell 144:310.e1 |
| Cairns, Bradley R (2009) The logic of chromatin architecture and remodelling at promoters. Nature 461:193-8 |
| Szerlong, Heather; Hinata, Kaede; Viswanathan, Ramya et al. (2008) The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol 15:469-76 |
Showing the most recent 10 out of 29 publications
