LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells.
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AbstractLong 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.
All Author(s) ListJiajian Zhou, Suyang Zhang, Huating Wang, Hao Sun
Journal nameNucleic Acids Research
Year2017
Month4
Day4
Volume Number45
Issue Number12
PublisherOxford University Press
ISSN0305-1048
LanguagesEnglish-United Kingdom
Keywordsembryonic stem cells, genes, mice, transcription factor, rna, micro rna, myoblasts, inference, skeletal myocytes, modified barium swallow

Last updated on 2020-07-08 at 01:46