Global and specific transcriptional repression by the histone H3 amino terminus in yeast

Abstract

The yeast CHA1 promoter is activated in the presence of serine or threonine. Activation requires the Cha4p activator, and it results in perturbation of a nucleosome that incorporates the TATA element under noninducing conditions. We show that in yeast lacking the amino terminus of histone H3, the promoter is constitutively active and the chromatin is concomitantly perturbed. This derepression occurs in the absence of elevated intracellular levels of serine or threonine and is not observed in cells lacking Rpd3p, Tup1p, or the amino terminus of histone H4. Furthermore, derepression in the absence of the H3 amino terminus requires the primary activator of this promoter, Cha4p, which we show by chromatin immunoprecipitation to be constitutively bound to the CHA1 promoter in WT yeast. Thus, the H3 amino terminus is required to prevent Cha4p from activating CHA1 in the absence of inducer. We also present results of a microarray experiment showing that the H3 amino terminus has a substantial repressive effect on a genome-wide scale. The principal protein components of chromatin are the histones. The four core histones, H2A, H2B, H3, and H4, can be divided into central structured domains and relatively unstructured amino and, in some cases, carboxyl-terminal regions, often referred to as the histone tails (1, 2). These latter regions do not contribute to core nucleosome structure (3), but are subject to numerous posttranslational modifications that contribute to multiple aspects of chromatin function (4-6). Specific modifications have been correlated with transcriptional activation and others with repression, including the formation of stably repressed domains of heterochromatin (7).One approach to studying the role of the histone tails in transcriptional regulation has been to focus on specific histonemodifying enzymes, or specific residues in the histone amino termini. An alternative, complementary approach has been to examine the effects of deleting individual histone amino termini. Such work has shown that in budding yeast (Saccharomyces cerevisiae), the individual histone amino termini are dispensable, but the H3 and H4 tails cannot be simultaneously removed without loss of viability, although they can be interchanged (8)(9)(10)(11). Other experiments have shown that the H3 and H4 tails are involved in silencing at telomeres and the silent mating-type loci (12, 13), and have implicated the H3 and H4 amino termini in both positive and negative aspects of gene regulation (14)(15)(16)(17).In this work we demonstrate a role for the histone H3 amino terminus in the regulation of the CHA1 promoter in yeast. Our initial interest in the CHA1 promoter stems from its tightly regulated chromatin structure. In its uninduced state, the CHA1 TATA element is incorporated near the center of a positioned nucleosome, and this nucleosome is perturbed on activation of CHA1 by increased intracellular levels of serine or threonine (18). Nucleosome perturbation requires the principal CHA1 activator, Cha4p, and can be elicited under cond...

Mediator, TATA-binding Protein, and RNA Polymerase II Contribute to Low Histone Occupancy at Active Gene Promoters in Yeast

“…CHA1 activation is essentially abolished at the restrictive temperature in yeast harboring a temperature-sensitive mutation in the essential Mediator subunit Srb4/Med17, and recruitment of PIC components TBP, Kin28, and Pol II, is greatly impaired (11). Induction of CHA1 also results in recruitment of the Swi/Snf complex and in remodeling of a nucleosome that incorporates the TATA element (11,(13)(14)(15). Surprisingly, this nucleosome remodeling, which is accompanied by histone eviction, occurs normally in swi/snf mutant yeast (11,14).…”

Redundant Mechanisms Are Used by Ssn6-Tup1 in Repressing Chromosomal Gene Transcription in Saccharomyces cerevisiae

“…However, mutating a single histone tail, as was done in the mentioned studies, may not be as disruptive to chromatin structure as deleting ISW2. Alternatively, deleting histone tails can affect activation pathways (54,55), and the derepressive effects of these mutations could be overshadowed by the positive role histone tails in activation. Our strategy, disrupting positioning using the ⌬isw2 mutation, leaves the histone tails intact and should not alter other functions of the tails.…”

Promoter-dependent Roles for the Srb10 Cyclin-dependent Kinase and the Hda1 Deacetylase in Tup1-mediated Repression inSaccharomyces cerevisiae

“…In addition, our own initial microarray analysis of a strain containing this internally deleted Tup1 allele (⌬129 -282aa) revealed no affect on Tup1-mediated repression (unpublished data). Similarly, microarrays of a strain with the histone H3 tail deleted (⌬1-28) show that the tails are important for the repression of a large set of genes but that only a minority of these are repressed by Tup1 (Sabet et al, 2003).…”