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Functional classification of long non-coding RNAs by k-mer content.
Kirk, Jessime M; Kim, Susan O; Inoue, Kaoru; Smola, Matthew J; Lee, David M; Schertzer, Megan D; Wooten, Joshua S; Baker, Allison R; Sprague, Daniel; Collins, David W; Horning, Christopher R; Wang, Shuo; Chen, Qidi; Weeks, Kevin M; Mucha, Peter J; Calabrese, J Mauro.
Affiliation
  • Kirk JM; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Kim SO; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Inoue K; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Smola MJ; National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
  • Lee DM; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Schertzer MD; National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
  • Wooten JS; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Baker AR; Ribometrix, Durham, NC, USA.
  • Sprague D; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Collins DW; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Horning CR; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Wang S; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Chen Q; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Weeks KM; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Mucha PJ; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Calabrese JM; Harvard Medical School, Ph.D. Program in Biological and Biomedical Sciences, Boston, MA, USA.
Nat Genet ; 50(10): 1474-1482, 2018 10.
Article in En | MEDLINE | ID: mdl-30224646
ABSTRACT
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
Subject(s)

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Sequence Analysis, RNA / Nucleotide Motifs / RNA, Long Noncoding Limits: Animals / Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2018 Document type: Article Affiliation country:

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Sequence Analysis, RNA / Nucleotide Motifs / RNA, Long Noncoding Limits: Animals / Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2018 Document type: Article Affiliation country: