Regulation of the Swi/Snf Chromatin Remodeling Complexes by the Non-Catalytic Subunits

The primary unit of eukaryotic DNA packaging is a nucleosome, which contains ∼150 bp of DNA wrapped around an octamer of histone proteins. This packaging restricts accessibility for transcription, replication, repair, and recombination. ATP-dependent chromatin remodeling complexes play a key role in regulating this accessibility. The catalytic subunits of these complexes use ATP, to alter histone-DNA and histone-histone interactions. Interestingly, the ATPase subunits alone carry out most of the remodeling activities of the entire complexes. This raises the question, of what are the functions of the non-catalytic subunits. Two hypotheses are: (i) non-catalytic subunits enhance the biochemical activity of the catalytic subunit, and (ii) non-catalytic subunits facilitate targeted localization. In Chapter 2, mechanistic roles of the non-catalytic subunits were elucidated. Comparing the hSWI/SNF complex with Brg1, its ATPase subunit, revealed that the non-catalytic subunits do not simply promote an active conformation of Brg1, but rather, enhance discrete steps in the remodeling reaction. Minimal complexes containing, Baf155, Baf170, and Ini1 were sufficient to lower the KM for nucleosomes, suggesting that these non-catalytic subunits help stabilize nucleosome binding. Overall, the data reveal that non-catalytic subunits have important mechanistic roles, including distinguishing between nucleotide states. In Chapter 3, other roles of non-catalytic subunits were identified, following a novel acetylation on the RSC complex, the yeast homolog of hSWI/SNF. Rsc4, the acetylated subunit, contains two bromodomains (BDs). BD1 has been previously shown to bind the acetylation mark when BD2 is not bound to acetylated H3K14 tails. However, we find that acetylation of Rsc4 does not modulate RSC's ability to recognize H3-acetylated nucleosomes. Instead, we found that high Rsc4 acetylation levels as maintained by BD1, are critical for resistance to DNA damage, especially in the absence of another remodeler, INO80. Further, cells lacking Rsc4 acetylation and NHP10, a unique INO80 subunit, have delayed S-phase progression and HU sensitivity, revealing a role for the RSC complex and its acetylation in resistance to replication stress. This study suggests that non-catalytic subunits can specify remodeler participation in cellular processes, distinct from enzymatic functions.