title: Human transcriptional interactome of chromatin contribute to gene co-expression.
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.
authors.affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Dong
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Yunqin
authors.initials: Y
authors.lastname: Chen
authors.forename: Guohui
authors.initials: G
authors.lastname: Ding
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D002877:Chromosomes, Human / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D009690:Nucleic Acid Conformation; D011485:Protein Binding / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D014157:Transcription Factors