Proteomic and genomic characterization of chromatin complexes at a boundary

Abstract

We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin. These assemblies contain characteristic stretches of DNA that flank particular regions of silent chromatin, as well as five distinctively modified histones and a set of protein complexes. The complexes consist of at least 15 chromatin-associated proteins, including DNA pol ɛ, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase. We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

Functional characterization of ATAD2 as a new cancer/testis factor and a predictor of poor prognosis in breast and lung cancers

“…With this respect, an alternative role of Atad2-K5ac binding could be its ability to antagonize the propagation of deacetylase complexes such as SMRT/HDAC3 and act as a boundary. This is in fact a very plausible mechanism as the yeast Atad2 ortholog, Yta7, has been shown to be a crucial component of complexes, which bind discrete regions of the genome including known boundaries between silent and active chromatin (Tackett et al, 2005).…”

“…The analysis of the encoded protein revealed the presence of a bromodomain and an ATPase domain of the AAA family ('ATPases associated with diverse cellular activities') suggesting functions related to genome regulation. Accordingly, work on its yeast ortholog showed its role in the maintenance of boundaries, critical for the functional organization of the genome in Saccaromyces cerevisiae (Jambunathan et al, 2005;Tackett et al, 2005;Fillingham et al, 2009), as well as in the transcriptional regulation of histone genes (Gradolatto et al, 2008). In addition, a genetic screen in Caenorabditis elegans suggests its involvement in the silencing of repeated transgenes (Tseng et al, 2007).…”

Unexpected Function of the Glucanosyltransferase Gas1 in the DNA Damage Response Linked to Histone H3 Acetyltransferases in Saccharomyces cerevisiae

“…Loss of SAS3 leads to a decrease of H3K14Ac, primarily at genes involved in cell cycle regulation and cell division (Rosaleny et al 2007). Sas3 physically interacts with Chk1 (Liu et al 2000), a Mec1 DNA damage pathway effector kinase and Dpb4, which regulates DNA replication and telomere silencing (Tackett et al 2005). As noted above, Sas3 physically associates with the FACT remodeling complex via interaction with the N terminus of Spt16 (John et al 2000), which is necessary for the DNA replication stress response (O'Donnell et al 2004).…”

“…Whereas Gcn5 has been studied extensively, less is known about Sas3, due in part to the functional overlaps with Gcn5 as well as the limited independent phenotypes defined for SAS3 mutants. Deletion of SAS3 leads to a modest increase in silencing at the HM loci (Reifsnyder et al 1996) and Sas3 localizes at the boundary of the HM loci, blocking the spread of silent chromatin (Tackett et al 2005). Sas3 physically associates with the N terminus of Spt16, a subunit of the FACT elongation complex (John et al 2000), which is essential for recovery from replication stress (O'Donnell et al 2004) and boundary formation (Tackett et al 2005).…”

Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation

“…HTA2-HTB2, the fourth histone gene pair, does not have a NEG region and is regulated in a HIR-independent manner. At HIR-dependent promoters, HIR recruits other histone chaperones, Asf1 and Rtt106, as well as the chromatin boundary protein Yta7 (8,9) and the remodel structure of chromatin (RSC) ATP-dependent chromatin-remodeling complex (10), which together assemble repressive chromatin, blocking recruitment of RNAPII (11,12). In S phase, this repressive chromatin is overcome, allowing recruitment of RNAPII and activation of transcription.…”