Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China.
BMC Genomics. 2010 Dec 14;11:704. doi: 10.1186/1471-2164-11-704.
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.
染色质的转录互作组是基因转录调控的重要机制之一。通过染色质构象捕获和 3D FISH 实验，已经报道了几个序列较远的基因甚至是染色体间基因之间的染色质相互作用案例。然而，在基因组水平上，仍然很少有证据支持这些机制。最近，基于 Hi-C 实验，展示了人类细胞中染色质相互作用的全基因组图谱。它为分析转录互作组的机制是否普遍提供了有用的材料。
这里的主要工作是证明转录互作组对基因共表达的影响是否存在于基因组水平上。在控制转录因子控制相似性（TCS）的影响的同时，我们测试了 Hi-C 相互作用与基因共表达率（由 COXPRESdb 提供）之间的相关性，这些基因对是在不同细胞类型中具有相似 Hi-C 相互作用等级的内染色质基因对。我们使用了 6084 个具有 TF 注释和共表达信息的基因，并将它们匹配到 273458 对具有不同细胞类型中相似 Hi-C 相互作用等级的基因对中。结果表明，共表达与染色质相互作用密切相关。使用 GO 注释的进一步分析揭示了基因功能相似性、Hi-C 相互作用及其共表达之间的潜在相关性。
根据本研究的结果，内染色质互作组可能与基因功能有关，并与共表达相关。这项研究为阐明转录互作组对转录调控的影响提供了证据。
