title: The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features.
abstract: Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions remain poorly understood. Here we took the human and mouse lncRNAs that were experimentally determined to have physical interactions with Polycomb repressive complex 2 (PRC2), and systematically investigated the sequence features of these lncRNAs by developing a new computational pipeline for sequences composition analysis, in which each sequence is considered as a series of transitions between adjacent nucleotides. Through that, PRC2-binding lncRNAs were found to be associated with a set of distinctive and evolutionarily conserved sequence features, which can be utilized to distinguish them from the others with considerable accuracy. We further identified fragments of PRC2-binding lncRNAs that are enriched with these sequence features, and found they show strong PRC2-binding signals and are more highly conserved across species than the other parts, implying their functional importance.
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.|Graduate University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Shiqi
authors.initials: S
authors.lastname: Tu
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.|Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
authors.forename: Guo-Cheng
authors.initials: GC
authors.lastname: Yuan
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Shao
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D005786:Gene Expression Regulation; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D051379:Mice; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism*; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism*; D012372:ROC Curve
chemical_list: D062085:RNA, Long Noncoding; D063151:Polycomb Repressive Complex 2