title: Integrating epigenetic marks for identification of transcriptionally active miRNAs.
abstract: MicroRNAs have been identified as important regulators involved in biological processes and human diseases. We proposed a computational approach to systematic identification of active promoters of miRNAs by active models using epigenetic characteristics at active promoters of protein-coding genes together with a genomic context-based filtering step in nine human cell types, which were validated to exhibit greater conservation, more overlap with CAGE-identified TSSs, more conserved TFBSs and higher transcription factor binding signal intensities. Furthermore, expression analysis showed discordance between transcriptional activation of miRNAs and expression of their precursor and mature forms, indicating that precursor and mature miRNA expression is insufficient to account for transcriptional activation of miRNAs. Compared to other methods, our approach identified higher percentages of active miRNAs with CAGE-detected TSS activity and primary transcript expression, further supporting the validity of our approach, which will be valuable to understand the biological roles of miRNAs in specific cell contexts.
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Yun
authors: Y
authors: Xiao
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Tingting
authors: T
authors: Liu
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Hongying
authors: H
authors: Zhao
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Xiang
authors: X
authors: Li
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Jinxia
authors: J
authors: Guan
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Chaohan
authors: C
authors: Xu
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Yanyan
authors: Y
authors: Ping
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Huihui
authors: H
authors: Fan
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Li
authors: L
authors: Wang
authors: Department of Neurology, The Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150086, China.
authors: Tingting
authors: T
authors: Zhao
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Yanling
authors: Y
authors: Lv
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Jing
authors: J
authors: Hu
authors: Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Key Laboratory of Medical Genetics, Harbin Medical University, Heilongjiang Higher Education Institutions, Harbin 150081, China.
authors: Xin
authors: X
authors: Yu
authors: Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Key Laboratory of Medical Genetics, Harbin Medical University, Heilongjiang Higher Education Institutions, Harbin 150081, China. Electronic address: JY8085@yahoo.com.cn.
authors: Yan
authors: Y
authors: Jin
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. Electronic address: lixia@hrbmu.edu.cn.
authors: Xia
authors: X
authors: Li
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology; D044127:Epigenesis, Genetic; D057890:Epigenomics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D005819:Genetic Markers; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D016015:Logistic Models; D035683:MicroRNAs / Q000235:genetics*; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D015533:Transcriptional Activation
chemical_list: D005819:Genetic Markers; D035683:MicroRNAs
keywords: Epigenetic; Promoter; Transcriptionally active; miRNA