Human transcriptional interactome of chromatin contribute to gene co-expression

Xiao Dong, Chao Li, Yunqin Chen, Guohui Ding, Yixue Li

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.

Original languageEnglish (US)
Article number704
JournalBMC Genomics
Volume11
Issue number1
DOIs
StatePublished - Dec 14 2010
Externally publishedYes

Fingerprint

Chromatin
Gene Expression
Genes
Genomics
Transcription Factors
Genome
Research

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Human transcriptional interactome of chromatin contribute to gene co-expression. / Dong, Xiao; Li, Chao; Chen, Yunqin; Ding, Guohui; Li, Yixue.

In: BMC Genomics, Vol. 11, No. 1, 704, 14.12.2010.

Research output: Contribution to journalArticle

Dong, Xiao ; Li, Chao ; Chen, Yunqin ; Ding, Guohui ; Li, Yixue. / Human transcriptional interactome of chromatin contribute to gene co-expression. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
@article{232c89c0de0e44ef929eed03ff2dbda8,
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.",
author = "Xiao Dong and Chao Li and Yunqin Chen and Guohui Ding and Yixue Li",
year = "2010",
month = "12",
day = "14",
doi = "10.1186/1471-2164-11-704",
language = "English (US)",
volume = "11",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Human transcriptional interactome of chromatin contribute to gene co-expression

AU - Dong, Xiao

AU - Li, Chao

AU - Chen, Yunqin

AU - Ding, Guohui

AU - Li, Yixue

PY - 2010/12/14

Y1 - 2010/12/14

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=78649983246&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78649983246&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-11-704

DO - 10.1186/1471-2164-11-704

M3 - Article

C2 - 21156067

AN - SCOPUS:78649983246

VL - 11

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 704

ER -