Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

Abstract

Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (−1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and −1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics.

Nucleosome Positioning and Its Role in Gene Regulation in Yeast

“…The current studies suggest that almost all eukaryotic organisms hold the nucleosome organization characteristics at the 5′ end of gene, namely a NFR lanked by two (+1 and −1) wellpositioned nucleosomes and followed by an array of nucleosomes downstream of TSSs [37,70,79]. But compared with multicellular organisms ly, worm, and human, yeast is very simple.…”

“…But yeast lacks the feature since its genomic DNA does not include introns. Moreover, upon stress or mutation, nucleosome dynamics frequently occurs at promoters in yeast cells [70]. But in human cells, the nucleosomes alter mainly at enhancers [82,83].…”

“…We examined the efect of substituting modiiable residues of four core histones with the non-modiiable residue alanine on nucleosome dynamics [70]. We mapped the genome-wide nucleosomes in 22 histone mutants of S. cerevisiae and compared the nucleosome alterations relative to the wild-type strain.…”

“…For single-end MNase-seq data, one method to make nucleosome proile is as follows [70]. First, the length of each read was extended 73 bp in the 3′ direction, and the Watson-strand reads and Crick-strand reads were oppositely shifted 73 bp.…”

“…Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome (B) Diference signiicance of nucleosome occupancy at telomeres and centromeres between each mutant and the wildtype strain. All P-values (−log10) were calculated with a two-sample t-test [70].…”