ATP-dependant chromatin remodeling complexes play an important role in the regulation of gene expression but their physiological targets, the way they are recruited and their function at those targets are mostly unknown. Here we use the genome-wide location analysis method to identify and characterize functional targets for the essential RSC (remodel the structure of chromatin) complex. Genomic binding sites were identified for five subunits of the ATP-dependent chromatin remodeling complex RSC.

Remarkably, the RSC complex specifically targets several gene classes, including the histones, S-phase specific cyclins, the nitrogen discrimination pathway and the carbohydrate metabolism. In addition to RNA polymerase II-transcribed promoters, RSC is also found at tRNA promoters, suggesting a role in RNA polymerase III transcription. Our data also show that Rsc1, Rsc2, and Rsc3, which have been shown to purify in different complexes in vitro, have similar location profiles in vivo. At the HTA1/HTB1 promoter, RSC is specifically recruited by the co-repressors Hir1 and Hir2 in a manner that correlates with transcriptional inactivity. On the other hand, RSC binds to genes involve in the TCA cycle, glycogen synthesis and trehalose synthesis concurrent with transcriptional activation. Therefore, it appears that RSC can be recruited by both transcription activators and repressors in vivo. Our study uncovers novel RSC targets and implicate RSC involvement in transcriptional processes.