title: Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data.
abstract: MicroRNAs (miRNAs) are critical small non-coding RNAs that regulate gene expression by hybridizing to the 3'-untranslated regions (3'-UTR) of target mRNAs, subsequently controlling diverse biological processes at post-transcriptional level. How miRNA genes are regulated receives considerable attention because it directly affects miRNA-mediated gene regulatory networks. Although numerous prediction models were developed for identifying miRNA promoters or transcriptional start sites (TSSs), most of them lack experimental validation and are inadequate to elucidate relationships between miRNA genes and transcription factors (TFs). Here, we integrate three experimental datasets, including cap analysis of gene expression (CAGE) tags, TSS Seq libraries and H3K4me3 chromatin signature derived from high-throughput sequencing analysis of gene initiation, to provide direct evidence of miRNA TSSs, thus establishing an experimental-based resource of human miRNA TSSs, named miRStart. Moreover, a machine-learning-based Support Vector Machine (SVM) model is developed to systematically identify representative TSSs for each miRNA gene. Finally, to demonstrate the effectiveness of the proposed resource, an important human intergenic miRNA, hsa-miR-122, is selected to experimentally validate putative TSS owing to its high expression in a normal liver. In conclusion, this work successfully identified 847 human miRNA TSSs (292 of them are clustered to 70 TSSs of miRNA clusters) based on the utilization of high-throughput sequencing data from TSS-relevant experiments, and establish a valuable resource for biologists in advanced research in miRNA-mediated regulatory networks.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Chien
authors.forename: Yi-Ming
authors.initials: YM
authors.lastname: Sun
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chang
authors.forename: Pei-Yun
authors.initials: PY
authors.lastname: Chiang-Hsieh
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.forename: Wei-Chih
authors.initials: WC
authors.lastname: Tsai
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Ann-Ping
authors.initials: AP
authors.lastname: Tsou
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D002460:Cell Line; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D017423:Sequence Analysis, RNA; D016324:Sequence Tagged Sites; D060388:Support Vector Machine; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; C531907:MIRN122 microRNA, human; D035683:MicroRNAs; D012319:RNA Polymerase II