Histone modifications influence chromatin modifying and chromatin remodeling complexes

Chromatin condenses DNA and packages it into the nucleus. The fundamental unit of chromatin is the nucleosome, which compacts and forms higher order structures. Chromatin structure affects transcription, DNA replication and DNA repair. For gene expression, chromatin is dynamically modulated by chromatin modifying complexes and chromatin remodeling complexes. The histone code hypothesis predicts that modifications not only dictate the inheritance of chromatin states, but also that combinations of modifications recognized by protein-interaction domains are important for recruiting cofactors that alter chromatin structure. For over 40 years, histone acetylation has been associated with gene activation. Moreover, the discovery of histone acetyl transferase (HAT) complexes has implicated acetylation in transcription, DNA repair and even silencing. The SAGA complex is a 1.8 MDa multisubunit HAT complex that is recruited by activator at promoters. As the catalytic subunit of SAGA, Gcn5 acetylates promoter nucleosomes and produces a peaked acetylation profile upon gene induction. Moreover, the Gcn5 bromodomain is required for retention on acetylated nucleosomes. We test the importance of the Gcn5 bromodomain in restricting SAGA acetylation to the promoter using the scanning in vitro chromatin immunoprecipitation assay. The Gcn5 bromodomain does not significantly affect the nucleosomal acetylation profile of SAGA, even when the activator is removed from the array. While the Spt7 bromodomain does not retain SAGA on acetylated nucleosomes in vitro, its evolutionary conservation in yeast suggests that it may help retain SAGA on acetylated nucleosomes in vivo. When tested on phenotypic screens, the Spt7 bromodomain mutant and the Spt7 and Gcn5 double bromodomain mutant have a slight phenotype.;The accumulation of acetylated histones at the promoter signals for the recruitment of other cofactors. SAGA and the ATP dependent chromatin remodeler, SWI/SNF functioned cooperatively in the activation of several genes in budding yeast. At the PHO5 promoter, both SAGA and SWI/SNF are important for timely removal of nucleosomes from the promoter. The loss of SWI/SNF results in the accumulation of H3K9 acetylated histones at this promoter, which is also an acetylation site for SAGA. Thus, SAGA acetylation at the promoter may recruit SWI/SNF and promote the displacement of acetylated nucleosomes. We directly test the influence of SAGA acetylation on SWI/SNF nucleosome displacement using several assays on the immobilized nucleosome array in vitro . SWI/SNF not only displaces acetylated nucleosomes, but it also targets promoter acetylated nucleosomes in the absence of activator. More important, SWI/SNF displacement of acetylated nucleosomes correlates with an increase in accessible DNA at the promoter.