Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae

Yangyang Deng,Jiang Wang,Zhiming Dai,Qian Xiang,Jihua Feng,Xianhua Dai,Caisheng He

doi:10.1186/1471-2164-11-550

Abstract

BackgroundNeighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear.ResultsWe investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions.ConclusionsThe results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.

Highlights

Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time
The results show that neighboring genes have similar histone modifications, and neighboring pairs of similar modifications exhibit similar expression
This study, for the first time, used the autocorrelation analysis to investigate the similarity of histone modification between neighboring genes

Summary

Introduction

Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. The extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear. Similar expression levels or expression patterns have been found in neighboring gene pairs in various eukaryotic genomes [1,6,7]. The coexpression sharing similar regulatory elements and chromatin environment have been proposed as two major factors responsible for coexpression of neighboring genes but the underlying mechanism is unclear [1,8,9]. Neighboring gene pairs in the budding yeast Saccharomyces cerevisiae exhibit stronger coexpression than random pairs [10]. Whole-genome expression data analysis has shown that divergent pairs (when the transcriptional directions of immediate neighboring pairs are divergent, i.e. ¬ ®)

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Discussion

Conclusion