Comparative Studies of Genome-Wide Maps of Nucleosomes between Deletion Mutants of elp3 and hos2 Genes of Saccharomyces cerevisiae

Takashi Matsumoto,Hirofumi Yoshikawa,Hiromi Nishida,Choong-Soo Yun,Laura Rusche

doi:10.1371/journal.pone.0016372

Takashi Matsumoto, Hirofumi Yoshikawa + Show 3 more

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https://doi.org/10.1371/journal.pone.0016372

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Journal: PloS one	Publication Date: Jan 28, 2011
Citations: 23	License type: CC BY 4.0

Affiliation: Tokyo University of Agriculture, The University of Tokyo

Abstract

In order to elucidate the influence of histone acetylation upon nucleosomal DNA length and nucleosome position, we compared nucleosome maps of the following three yeast strains; strain BY4741 (control), the elp3 (one of histone acetyltransferase genes) deletion mutant, and the hos2 (one of histone deactylase genes) deletion mutant of Saccharomyces cerevisiae. We sequenced mononucleosomal DNA fragments after treatment with micrococcal nuclease. After mapping the DNA fragments to the genome, we identified the nucleosome positions. We showed that the distributions of the nucleosomal DNA lengths of the control and the hos2 disruptant were similar. On the other hand, the distribution of the nucleosomal DNA lengths of the elp3 disruptant shifted toward shorter than that of the control. It strongly suggests that inhibition of Elp3-induced histone acetylation causes the nucleosomal DNA length reduction. Next, we compared the profiles of nucleosome mapping numbers in gene promoter regions between the control and the disruptant. We detected 24 genes with low conservation level of nucleosome positions in promoters between the control and the elp3 disruptant as well as between the control and the hos2 disruptant. It indicates that both Elp3-induced acetylation and Hos2-induced deacetylation influence the nucleosome positions in the promoters of those 24 genes. Interestingly, in 19 of the 24 genes, the profiles of nucleosome mapping numbers were similar between the two disruptants.

Highlights

Eukaryotic genomic DNA is packaged with histone proteins to form chromatin [1], the most fundamental repeating unit of which is the nucleosome [2]
The precise organization of this chromatin is of utmost importance for the maintenance of eukaryotic genomic DNA
Distribution of nucleosomal DNA lengths We identified 1578348, 789257, and 2664981 mononucleosomal DNA fragments of strain BY4741, the elp3 deletion mutant, and the hos2 deletion mutant, respectively

Summary

Introduction

Eukaryotic genomic DNA is packaged with histone proteins to form chromatin [1], the most fundamental repeating unit of which is the nucleosome [2]. The precise organization of this chromatin is of utmost importance for the maintenance of eukaryotic genomic DNA. Nucleosomes consist of an octamer of histones, around which the DNA is wrapped [3]. Nucleosomal histone proteins are post-translationally modified [4]. Reversible histone acetylation, which is regulated by histone acetyltransferase [5] and deacetylase [6,7], is one such modification. The acetylation and deacetylation of the core histone tails play an important role in the regulation of transcription [8,9]. A histone-modifying protein complex consists of a catalytic subunit and the associated subunits. The budding yeast Saccharomyces cerevisiae has 62 subunits including 15 histone acetyltransferase catalytic subunits and 12 histone deacetylase catalytic subunits [10]

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