Comparison of the structure and cell cycle expression of mRNAs encoded by two histone H3-H4 loci in Saccharomyces cerevisiae.

Abstract

The haploid genome of Saccharomyces cerevisiae contains two nonallelic sets of histone H3 and H4 gene pairs, termed the copy I and copy I loci. The structures of the mRNA transcripts from each of these four genes were examined by nuclease protection and primer extension mapping. For each gene, several species of mRNAs were identified that differed in the lengths of their S' and 3' untranslated regions. The cell cycle accumulation pattern of the H3 and H4 mRNAs was determined in cells from early-exponential-growth cultures fractionated by centrifugal elutriation. The RNA trnscripts from all four genes were regulated with the cell division cycle, and btanscripts from the nonallelic gene copies showed tight temporal coordination. Cell cycle regulation did not depend on selection of a particular histone mRNA transcript since the ratio of the multiple species from each gene remained the same across the division cycle. Quantitative measurements showed significant differences in the amounts of mRNA expressed from the two nonallelic gene sets. The mRNAs from the copy 11 H3 and H4 genes were five to seven times more abundant than the mRNAs from the copy I genes. There was no dosage compensation in the steady-state levels of mRNA when either set of genes was deleted. In particular, there was no increase in the amount of copy I H3 or H4 transcripts in cells in which the high-abundance copy II genes were deleted.For most classes of histone, gene expression is regulated in a cell-cycle-dependent fashion, with the maximal amount of histone RNA and protein synthesis occurring in late G1 or early S phase (28, 37). The replacement or basal histone gene variants (49) and avian histone H5 (7) are notable exceptions to this rule. The cell cycle regulation of histone mRNA expression has been investigated in several systems and is likely to involve changes in the rate of gene transcription (14,17,32), changes in mRNA stability (15,17,40), and structural features of the mRNA transcripts and their templates (4, 25).The core histone genes of budding yeast, Saccharomyces cerevisiae, are organized as duplicate H2A-H2B and H3-H4 gene pairs (43). The four nonallelic chromosomal gene sets are unlinked and, at each locus, the paired genes are divergently transcribed (19, 45). The DNA sequences of analogous genes are highly conserved within the coding regions, but the 5' and 3' untranslated regions are divergent. The yeast core histone genes show a typical cell-divisioncycle-dependent pattern of expression. Both the rate of synthesis of new histone (23, 24) and the appearance of histone mRNA are periodic in the division cycle (20). There appear to be several mechanisms regulating expression of the genes, and both transcriptional and posttranscriptional controls have been proposed for the H2A and H2B genes (18,26,32,33).In this paper, we report the structure and cell cycle pattern of accumulation of the yeast histone H3 and H4 genes. These experiments addressed several aspects of H3 and H4 gene expression. First, we determined the structures of...

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.…”

Alterations in DNA Replication and Histone Levels Promote Histone Gene Amplification in Saccharomyces cerevisiae

“…Table 2. hhf1)D suppresses the need for the HTA2-HTB2 amplification, whereas (hhf2-hht2)D enhances its frequency. We note that previous studies showed that HHT1-HHF1 is expressed at a substantially lower level than HHT2-HHF2 (Cross and Smith 1988). These differences likely lead to the different phenotypes with respect to HTA2-HTB2 amplification (see discussion).…”

“…These differences are likely caused by the distinct effects that the two deletions have on H3-H4 levels because previous studies have shown that the two H3-H4 loci are transcribed at different levels, with HHT2-HHF2 producing five-to sevenfold more mRNA than HHT1-HHF1 (Cross and Smith 1988). Thus, the viability of the (hht1-hhf1)D (hta1-htb1)D double mutant suggests that the H3-H4 level in this mutant allows approximately normal stoichiometry between H2A-H2B and H3-H4, although the absolute histone levels may be reduced in the (hht1-hhf1)D (hta1-htb1)D double mutant compared to wild type.…”

A search for proteins that interact genetically with histone H3 and H4 amino termini uncovers novel regulators of the Swe1 kinase in Saccharomyces cerevisiae.

“…One possible role may be in repli cation-coupled nucleosome assembly during S phase (Kaufman and Botchan 1994;Kaufman et al 1995). A close temporal link between DNA synthesis and nucleo some assembly is reflected by the fact that histone syn thesis takes place in S phase (Hereford et al 1981;Cross and Smith 1988). We have demonstrated recently that the amino-termini of H3 and H4 are required for nucleo some assembly in a redundant fashion both in vivo and in vitro (Ling et al 1996).…”