Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information

Junbai Wang

doi:10.1186/1471-2164-12-172

Abstract

BackgroundIn parallel with the quick development of high-throughput technologies, in vivo (vitro) experiments for genome-wide identification of protein-DNA interactions have been developed. Nevertheless, a few questions remain in the field, such as how to distinguish true protein-DNA binding (functional binding) from non-specific protein-DNA binding (non-functional binding). Previous researches tackled the problem by integrated analysis of multiple available sources. However, few systematic studies have been carried out to examine the possible relationships between histone modification and protein-DNA binding. Here this issue was investigated by using publicly available histone modification data in yeast.ResultsTwo separate histone modification datasets were studied, at both the open reading frame (ORF) and the promoter region of binding targets for 37 yeast transcription factors. Both results revealed a distinct histone modification pattern between the functional protein-DNA binding sites and non-functional ones for almost half of all TFs tested. Such difference is much stronger at the ORF than at the promoter region. In addition, a protein-histone modification interaction pathway can only be inferred from the functional protein binding targets.ConclusionsOverall, the results suggest that histone modification information can be used to distinguish the functional protein-DNA binding from the non-functional, and that the regulation of various proteins is controlled by the modification of different histone lysines such as the protein-specific histone modification levels.

Highlights

In parallel with the quick development of high-throughput technologies, in vivo experiments for genome-wide identification of protein-DNA interactions have been developed
Some of the previous studies considered the effect of nucleosomes on transcription factors (TF)-DNA interactions, most of them ignored an important aspect that is closely associated with functional TF binding, that is, changes in chromatin structure are affected by histone modifications such as methylation and acetylation [14,15]
Histone acetylation (Kurdistani et al.) Figure 1 and Additional file 1 Figure S1 show the hierarchical clustering of t-values at open reading frame (ORF) and promoter

Summary

Introduction

In parallel with the quick development of high-throughput technologies, in vivo (vitro) experiments for genome-wide identification of protein-DNA interactions have been developed. Three major models have been proposed to explain the role of histone modification in genome regulation: 1) charge neutralization [20], by which histone modification can relax chromatin structure because of neutralizing positive charges on DNA; 2) histone code [21], by which combinatory histone modifications can regulate downstream gene functions; and 3) signaling pathway [22,23], by which multiple histone modifications can provide bi-stability and robustness through feedback loops Motivated by this unsolved question, a systematic study of associations between TF-DNA binding and histone modification in yeast was carried out by integrative analysis of diverse datasets [8,9,24,25,26,27]

Methods

Results

Conclusion