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Open Access Highly Accessed Research article

Human transcriptional interactome of chromatin contribute to gene co-expression

Xiao Dong12, Chao Li123, Yunqin Chen4, Guohui Ding15* and Yixue Li15*

Author Affiliations

1 Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China

2 Graduate School of Chinese Academy of Sciences, Beijing, PR China

3 School of Life Science, University of Science and Technology of China, Hefei, PR China

4 School of Life Sciences and Technology, Tongji University, Shanghai, PR China

5 Shanghai Center for Bioinformation Technology, Shanghai, PR China

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BMC Genomics 2010, 11:704  doi:10.1186/1471-2164-11-704

Published: 14 December 2010

Abstract

Background

Transcriptional interactome of chromatin is one of the important mechanisms in gene transcription regulation. By chromatin conformation capture and 3D FISH experiments, several chromatin interactions cases among sequence-distant genes or even inter-chromatin genes were reported. However, on genomics level, there is still little evidence to support these mechanisms. Recently based on Hi-C experiment, a genome-wide picture of chromatin interactions in human cells was presented. It provides a useful material for analysing whether the mechanism of transcriptional interactome is common.

Results

The main work here is to demonstrate whether the effects of transcriptional interactome on gene co-expression exist on genomic level. While controlling the effects of transcription factors control similarities (TCS), we tested the correlation between Hi-C interaction and the mutual ranks of gene co-expression rates (provided by COXPRESdb) of intra-chromatin gene pairs. We used 6,084 genes with both TF annotation and co-expression information, and matched them into 273,458 pairs with similar Hi-C interaction ranks in different cell types. The results illustrate that co-expression is strongly associated with chromatin interaction. Further analysis using GO annotation reveals potential correlation between gene function similarity, Hi-C interaction and their co-expression.

Conclusions

According to the results in this research, the intra-chromatin interactome may have relation to gene function and associate with co-expression. This study provides evidence for illustrating the effect of transcriptional interactome on transcription regulation.