title: Computational identification of putative lincRNAs in mouse embryonic stem cell.
abstract: As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5' ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features. Subsequently, 1,293 lincRNAs were corrected at their 5' ends using the putative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic and epigenetic features. Finally, 43 putative lincRNAs were annotated by Gene Ontology terms. In conclusion, this work provides a novel catalog of mouse ESCs-expressed lincRNAs with the relatively complete transcript length, which might be useful for the investigation of transcriptional and post-transcriptional regulation of lincRNA in mouse ESCs and even mammalian development.
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Lyu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Liu
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Hongjuan
authors.initials: H
authors.lastname: He
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Zhengbin
authors.initials: Z
authors.lastname: Han
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D000069550:Machine Learning; D051379:Mice; D008957:Models, Genetic; D000066450:Mouse Embryonic Stem Cells / Q000502:physiology*; D062085:RNA, Long Noncoding / Q000235:genetics*; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding