title: Identification of expressed and conserved human noncoding RNAs.
abstract: The past decade has shown mammalian genomes to be pervasively transcribed and identified thousands of noncoding (nc) transcripts. It is currently unclear to what extent these transcripts are of functional importance, as experimental functional evidence exists for only a small fraction. Here, we characterize the expression and evolutionary conservation properties of 12,115 known and novel nc transcripts, including structural RNAs, long nc RNAs (lncRNAs), antisense RNAs, EvoFold predictions, ultraconserved elements, and expressed nc regions. Expression levels are evaluated across 12 human tissues using a custom-designed microarray, supplemented with RNAseq. Conservation levels are evaluated at both the base level and at the syntenic level. We combine these measures with epigenetic mark annotations to identify subsets of novel nc transcripts that show characteristics similar to known functional ncRNAs. Few novel nc transcripts show both high expression and conservation levels. However, overall, we observe a positive correlation between expression and both conservation and epigenetic annotations, suggesting that a subset of the expressed transcripts are under purifying selection and likely functional. The identified subsets of expressed and conserved novel nc transcripts may form the basis for further functional characterization.
authors.forename: Morten Muhlig
authors.initials: MM
authors.lastname: Nielsen
authors.forename: Disa
authors.initials: D
authors.lastname: Tehler
authors.forename: Søren
authors.initials: S
authors.lastname: Vang
authors.forename: Frantisek
authors.initials: F
authors.lastname: Sudzina
authors.forename: Jakob
authors.initials: J
authors.lastname: Hedegaard
authors.forename: Iver
authors.initials: I
authors.lastname: Nordentoft
authors.forename: Torben Falck
authors.initials: TF
authors.lastname: Orntoft
authors.forename: Anders H
authors.initials: AH
authors.lastname: Lund
authors.forename: Jakob Skou
authors.initials: JS
authors.lastname: Pedersen
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000235:genetics; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D006801:Humans; D055029:Inverted Repeat Sequences; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D009928:Organ Specificity; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D002843:Chromatin; D022661:RNA, Untranslated
keywords: EvoFold predictions; comparative genomics; lncRNA; noncoding RNA; ultraconserved elements