TY - JOUR
T1 - Identification of expressed and conserved human noncoding RNAs
AU - Nielsen, Morten Muhlig
AU - Tehler, Disa
AU - Vang, Søren
AU - Sudzina, Frantisek
AU - Hedegaard, Jakob
AU - Nordentoft, Iver
AU - Orntoft, Torben Falck
AU - Lund, Anders H.
AU - Pedersen, Jakob Skou
PY - 2014/2
Y1 - 2014/2
N2 - 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.
AB - 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.
KW - Base Sequence
KW - Chromatin
KW - Conserved Sequence
KW - Expressed Sequence Tags
KW - Humans
KW - Inverted Repeat Sequences
KW - Molecular Sequence Annotation
KW - Oligonucleotide Array Sequence Analysis
KW - Open Reading Frames
KW - Organ Specificity
KW - RNA, Untranslated
KW - Transcriptome
KW - Journal Article
KW - Research Support, Non-U.S. Gov't
U2 - 10.1261/rna.038927.113
DO - 10.1261/rna.038927.113
M3 - Journal article
C2 - 24344320
SN - 1355-8382
VL - 20
SP - 236
EP - 251
JO - RNA
JF - RNA
IS - 2
ER -