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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



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.


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.


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.