title: Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues.
abstract: 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.
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China.
authors.forename: Zhiyun
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Department of Biology, Lakehead University, Oliver Road, Thunder Bay, Ontario.
authors.forename: Miranda
authors.initials: M
authors.lastname: Maki
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China.
authors.forename: Ruofan
authors.initials: R
authors.lastname: Ding
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China.
authors.forename: Bao
authors.initials: B
authors.lastname: Zhang
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China.
authors.forename: Lili
authors.initials: L
authors.lastname: Xiong
mesh_terms: D002874:Chromosome Mapping; D053263:Gene Regulatory Networks / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014781:Viscera / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors