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.
Bibliographical noteFunding Information:
We thank Prof. Xiangyin Kong, Dr. Guangyong Zheng, Mr. Zhen Wang, Mr. Jingxuan Zhang, and Ms. Tingyan Zhong for their helpful comments and suggestions. This research was supported by grants from National High-Tech R&D Program (863) (2006AA02Z334, 2007DFA31040), State key basic research program (973) (2006CB910705, 2010CB529206, 2011CBA00801), Research Program of CAS (KSCX2-YW-R-112, KSCX2-YW-R-190), National Natural Science Foundation of China (30900272) and Special Start-up Fund for CAS President Award Winner (to G. Ding).