Direct Interplay among Histones, Histone Chaperones, and a Chromatin Boundary Protein in the Control of Histone Gene Expression

Abstract

In Saccharomyces cerevisiae, the histone chaperone Rtt106 binds newly synthesized histone proteins and mediates their delivery into chromatin during transcription, replication, and silencing. Rtt106 is also recruited to histone gene regulatory regions by the HIR histone chaperone complex to ensure S-phase-specific expression. Here we showed that this Rtt106:HIR complex included Asf1 and histone proteins. Mutations in Rtt106 that reduced histone binding reduced Rtt106 enrichment at histone genes, leading to their increased transcription. Deletion of the chromatin boundary element Yta7 led to increased Rtt106:H3 binding, increased Rtt106 enrichment at histone gene regulatory regions, and decreased histone gene transcription at the HTA1-HTB1 locus. These results suggested a unique regulatory mechanism in which Rtt106 sensed the level of histone proteins to maintain the proper level of histone gene transcription. The role of these histone chaperones and Yta7 differed markedly among the histone gene loci, including the two H3-H4 histone gene pairs. Defects in silencing in rtt106 mutants could be partially accounted for by Rtt106-mediated changes in histone gene repression. These studies suggested that feedback mediated by histone chaperone complexes plays a pivotal role in regulating histone gene transcription. Cell cycle-regulated transcription of the canonical histone genes is a hallmark of eukaryotic organisms. During S phase, a coordinated burst of histone gene transcription is required to double the level of histone proteins to package newly replicated DNA into chromatin (13,22). The tight coupling of both the timing and the level of histone gene expression with DNA synthesis is critical for cell viability. Mutations that perturb DNA replication lead to altered histone gene transcription (3, 23). Conversely, misregulation of the timing and/or level of histone gene expression leads to genomic instability and cell cycle defects (23,43). Consequently, cells have evolved a complex regulatory mechanism to repress histone gene transcription outside S phase and to promote a precise level of transcription during S phase.The Saccharomyces cerevisiae genome contains two nonallelic copies of each canonical histone gene which are organized in head-to-head pairs of H2A-H2B (HTA1-HTB1 and HTA2-HTB2) and H3-H4 (HHT1-HHF1 and HHT2-HHF2). Nucleosomes, the fundamental units of chromatin structure, contain two H2A/H2B dimers, one H3/H4 tetramer, and ϳ147 bp of DNA wrapped around the outer surface (37). Repression of histone transcription outside S phase is maintained by the HIR H3/H4 histone-protein chaperone complex, referred to here as the HIR complex (Hir1, Hir2, Hir3, and Hpc2). The HIR complex localizes to negative (NEG) sequence elements within the regulatory regions of HTA1-HTB1, 45,59). Although HTA2-HTB2 transcription is S-phase specific, its promoter does not contain NEG elements, and the factors involved in its HIRindependent repression are unknown (45). A recent study implicated two additional H3/H4 chaperones, Rtt106 ...

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

“…The role of histones in the DNA damage response is complex, such that even modest imbalances in histone levels can alter DNA damage sensitivity (see for example Gunjan and Verreault 2003;Sanders et al 2004;Du et al 2006). Whereas the duplicate histone loci are believed to be largely redundant, there are distinctions both at the level of dosage (Cross and Smith 1988;Libuda and Winston 2010) and in regulation of their expression (Zunder and Rine 2012). Our findings here and previous work of others (Sanders et al 2004;Du et al 2006) suggest that the HHT1-HHF1 locus may indeed have a unique function in DNA damage.…”

Transcription coordinates histone amounts and genome content

“…Moreover, three out of four core histone gene pairs, not including HTA2-HTB2, show negative feedback regulation of transcript concentration upon replication stress 14,28 . This feedback regulation is thought to be mediated by the HIR complex and to be dependent on HIR1 and RTT106 [29][30][31] . Thus, to test if HIRdependent sensing and feedback regulation of histone transcript concentration may also be responsible for the cell-volume-dependence of HIR-regulated histone genes, we measured the cellvolume-dependence of representative histone genes (HTB1, HTB2, HHF1, HHO1) in hir1∆ and rtt106∆ strains.…”

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

“…Because we detected all four HIR subunits in our mChIP of Spt10-TAP, we next used chromatin immunoprecipitation (ChIP) to test whether SPT10 is required for recruitment of HIR (Hir1-TAP), the HIR-dependent regulators RSC (Rsc8-TAP), SWI/SNF (Snf6), Rtt106-TAP, and Asf1-TAP, and the transcriptional activator Yta7 (Yta7-TAP) (8,11,13) to the promoter region of HTA1-HTB1 (Fig. 1A) (11).…”

“…In S phase, this repressive chromatin is overcome, allowing recruitment of RNAPII and activation of transcription. After recruitment of RNAPII, the AAA-ATPase Yta7 is important for efficient transcript elongation by evicting histones H3-H4 (11)(12)(13). Other chromatin remodelers also have roles in histone gene activation, including the SWI/SNF chromatin-remodeling complex, which activates NEG-dependent histone genes (14), and the histone-acetyltransferase (HAT) complex Rtt109-Vps75 (8).…”