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Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues

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WOS被引频次:69
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成果类型:
期刊论文
作者:
Guo, Zhiyun;Maki, Miranda;Ding, Ruofan;Yang, Yalan;Zhang, Bao;Xiong, Lili*
通讯作者:
Xiong, Lili
作者机构:
[Guo, Zhiyun; Ding, Ruofan; Yang, Yalan; Zhang, Bao; Xiong, Lili] School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
[Maki, Miranda] Department of Biology, Lakehead University, Oliver Road, Thunder Bay, Ontario
通讯机构:
[Xiong, Lili] Southwest Jiaotong Univ, Sch Life Sci & Bioengn, Chengdu 610031, Peoples R China.
语种:
英文
期刊:
SCIENTIFIC REPORTS
ISSN:
2045-2322
年:
2014
卷:
4
页码:
5150
文献类别:
WOS:Article;PUBMED:Journal Article
入藏号:
基金类别:
National Natural Science Foundation of China [31200999]; Fundamental Research Funds for the Central Universities [2682014CX049]
机构署名:
本校为第一且通讯机构
院系归属:
生命科学与工程学院
摘要:
Tissue-specific miRNAs (TS miRNA) specifically expressed in particular tissues play an important role in tissue identity, differentiation and function. However, transcription factor (TF) and TS miRNA regulatory networks across multiple tissues have not been systematically studied. Here, we manually extracted 116 TS miRNAs and systematically investigated the regulatory network of TF-TS miRNA in 12 human tissues. We identified 2,347 TF-TS miRNA regulatory relations and revealed that most TF binding sites tend to enrich close to the transcription start site of TS miRNAs. Furthermore, we found TS miRNAs were regulated widely by non-tissue specific TFs and the tissue-specific expression level of TF have a close relationship with TF-genes regulation. Finally, we describe TSmiR (http://bioeng.swjtu.edu.cn/TSmiR), a novel and web-searchable database that houses interaction maps of TF-TS miRNA in 12 tissues. Taken together, these observations provide a new suggestion to better understand the regulatory network and mechanisms of TF-TS miRNAs underlying different tissues.
参考文献:
Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298, 799–804 (2002).
Yu, H. & Gerstein, M. Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A. 103, 14724–14731 (2006).
Hobert, O. Gene regulation by transcription factors and microRNAs. Science. 319, 1785–1786 (2008).
Saito, Y., Suzuki, H. & Hibi, T. The role of microRNAs in gastrointestinal cancers. J Gastroenterol. 44 Suppl 19, 18–22 (2009).
Baek, D. et al. The impact of microRNAs on protein output. Nature. 455, 64–71 (2008).

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