An evolutionarily ‘young’ lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae

Edel M. Hyland; Henrik Molina; Kunal Poorey; Chunfa Jie; Zhi Xie; Junbiao Dai; Jiang Qian; Stefan Bekiranov; David T. Auble; Akhilesh Pandey; Jef D. Boeke

doi:10.1101/gad.2050311

An evolutionarily ‘young’ lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae

¹High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
²Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
³Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA;
⁴Wilmer Bioinformatics Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

↵Present addresses: ⁵Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA;
↵6 Center for Genome Regulation (CRG), Barcelona 08003, Spain;
↵7 School of Life Sciences, Tsinghua University, Beijing 100084, China.

Abstract

The DNA entry and exit points on the nucleosome core regulate the initial invasion of the nucleosome by factors requiring access to the underlying DNA. Here we describe in vivo consequences of eliminating a single protein–DNA interaction at this position through mutagenesis of histone H3 Lys 42 to alanine. This substitution has a dramatic effect on the Saccharomyces cerevisiae transcriptome in both the transcriptional output and landscape of mRNA species produced. We attribute this in part to decreased histone H3 occupancy at transcriptionally active loci, leading to enhanced elongation. Additionally we show that this lysine is methylated in vivo, and genetic studies of methyl-lysine mimics suggest that this modification may be crucial in attenuating gene expression. Interestingly, this site of methylation is unique to Ascomycota, suggesting a recent evolutionary innovation that highlights the evolvability of post-translational modifications of chromatin.