Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast

Abstract

Heterochromatin is a cytologically visible form of condensed chromatin capable of repressing genes in eukaryotic cells. For the yeast Saccharomyces cerevisiae, despite the absence of observable heterochromatin, there is genetic and chromatin structure data which indicate that there are heterochromatin-like repressive structures. Genes experience position effects at the silent mating loci and the telomeres, resulting in a repressed state that is inherited in an epigenetic manner. The histone H4 amino terminus is required for repression at these loci. Additional studies have indicated that the histone H3 N terminus is not important for silent mating locus repression, but redundancy of repressive elements at the silent mating loci may be responsible for masking its role. Here we report that histone H3 is required for full repression at yeast telomeres and at partially disabled silent mating loci, and that the acetylatable lysine residues of H3 play an important role in silencing.

HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription

“…Activity 5-fluoroorotic acid (5-FOA) (29). This assay is extremely sensitive in that a several-fold increase in URA3 expression can result in an increase of 6-7 orders of magnitude in 5-FOA sensitivity (18,29). Contrary to the predicted effect of increased histone acetylation, we find that both hda1⌬ and rpd3⌬ increased repression of URA3 integrated 2.1 kb (Fig.…”

“…Deletions and mutations of H4 lysines 5, 8, and 12 have little, if any, effect on heterochromatic silencing in yeast. However, a mutation at position 16 can strongly derepress silencing (15)(16)(17)(18). Lysine 16 has been shown to be involved in mediating the interaction between the histone H4 N terminus and silencing information regulator (SIR) repressors of yeast heterochromatin in vitro and in whole cell extracts (19,20).…”

Nucleosome Structural Transition during Chromatin Unfolding Is Caused by Conformational Changes in Nucleosomal DNA

“…This is strongly supported by the observation that a deletion of the histone H2B cross-linking domain changes the minichromosome topology in vivo, suggesting that this domain is required for the proper folding of DNA in the nucleosome (63). Deletion or substitution of a single amino acid in the cross-linking domain of histone H4 alters chromatin structure in vivo (63)(64)(65)(66), decreases the ability of yeast to mate, increases the duration of S phase (67)(68)(69)(70), and affects telomeric repression (71,72) as well as expression of a large number of yeast genes (64,65,(73)(74)(75). It should be mentioned also that the cross-linking domain of histone H4 contains sites for post-translational acetylation and phosphorylation (76) that may also be involved in the regulation of the interaction of this domain with DNA at different levels of chromatin activity and condensation rendering nucleosomes competent for transcription and/or replication.…”

Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate

“…Contrary to this assumption, H4 K16R mutations cause a strong loss of telomeric silencing and defects in HM silencing ( Fig. S2) (26,30), showing that the K16R mutation is not equivalent to a deacetylated lysine. We propose that H4 K16R suppresses the sas2Δ rpd3Δ lethality through its derepressing effect on telomeric silencing.…”

“…Such mutations have been shown previously to abrogate silencing ( Fig. S2) (30). The H4 K16R suppression may seem counterintuitive, given that mutations of lysine to arginine generally are thought to mimic the deacetylated state of the lysine residue and therefore would be expected to improve SIR binding and silencing.…”