title: LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells.
abstract: Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, we present a novel computational framework, lncFunNet (lncRNA Functional inference through integrated Network) that integrates ChIP-seq, CLIP-seq and RNA-seq data to predict, prioritize and annotate lncRNA functions. In mouse embryonic stem cells (mESCs), using lncFunNet we not only recovered most of the functional lncRNAs known to maintain mESC pluripotency but also predicted a plethora of novel functional lncRNAs. Similarly, in mouse myoblast C2C12 cells, applying lncFunNet led to prediction of reservoirs of functional lncRNAs in both proliferating myoblasts (MBs) and differentiating myotubes (MTs). Further analyses demonstrated that these lncRNAs are frequently bound by key transcription factors, interact with miRNAs and constitute key nodes in biological network motifs. Further experimentations validated their dynamic expression profiles and functionality during myoblast differentiation. Collectively, our studies demonstrate the use of lncFunNet to annotate and identify functional lncRNAs in a given biological system.
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.|Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Jiajian
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.|Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Suyang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.|Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Huating
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.|Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Sun
mesh_terms: D000465:Algorithms; D000818:Animals; D002454:Cell Differentiation; D005786:Gene Expression Regulation; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D018485:Muscle Fibers, Skeletal / Q000166:cytology / Q000378:metabolism*; D032446:Myoblasts / Q000166:cytology / Q000378:metabolism*; D059372:Nucleotide Motifs; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D014157:Transcription Factors