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

Abstract

Gene amplification, a process that increases the copy number of a gene or a genomic region to two or more, is utilized by many organisms in response to environmental stress or decreased levels of a gene product. Our previous studies in Saccharomyces cerevisiae identified the amplification of a histone H2A-H2B gene pair, HTA2-HTB2, in response to the deletion of the other H2A-H2B gene pair, HTA1-HTB1. This amplification arises from a recombination event between two flanking Ty1 elements to form a new, stable circular chromosome and occurs at a frequency higher than has been observed for other Ty1-Ty1 recombination events. To understand the regulation of this amplification event, we screened the S. cerevisiae nonessential deletion set for mutations that alter the amplification frequency. Among the deletions that increase HTA2-HTB2 amplification frequency, we identified those that either decrease DNA replication fork progression (rrm3D, dpb3D, dpb4D, and clb5D) or that reduce histone H3-H4 levels (hht2-hhf2D). These two classes are related because reduced histone H3-H4 levels increase replication fork pauses, and impaired replication forks cause a reduction in histone levels. Consistent with our mutant screen, we found that the introduction of DNA replication stress by hydroxyurea induces the HTA2-HTB2 amplification event. Taken together, our results suggest that either reduced histone levels or slowed replication forks stimulate the HTA2-HTB2 amplification event, contributing to the restoration of normal chromatin structure.

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.…”

G9a-mediated histone methylation regulates ethanol-induced neurodegeneration in the neonatal mouse brain

“…Many studies have revealed that histone levels are controlled by several distinct mechanisms, including transcriptional control (Osley, 1991) and protein stability through phosphorylation and ubiquitination (Singh et al, 2009), as well as acetylation and methylation (Strahl and Allis, 2000). Clearly, posttranslational modification of histone proteins have a profound effect on chromosome stability, transcription, cell growth and survival (Libuda and Winston, 2010). Many substrates for caspase-3 have been identified in the nucleus (Fischer et al, 2003) and caspase-3 is believed to play an important role in the nuclear morphological changes that occur in apoptotic cells (Kamada et al, 2005).…”

Regulation of Histone Gene Expression in Budding Yeast

“…When DNA synthesis is inhibited by hydroxyurea, histone message levels are drastically reduced. This reduction is transient; the message levels are restored as cells adapt to replication stress (Libuda and Winston 2010). Histone gene expression is rendered immune to hydroxyurea-mediated repression by deletion of the NEG region, by hir mutations, and by asf1 mutations, again with the exception of HTA2-HTB2 Osley and Lycan 1987;Xu et al 1992;Spector and Osley 1993;Spector et al 1997;Sutton et al 2001;Ng et al 2002).…”