Iver Kristiansen Nordentoft

Identification of expressed and conserved human noncoding RNAs

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Identification of expressed and conserved human noncoding RNAs. / Nielsen, Morten Muhlig; Theler, Disa; Vang, Søren; Sudzina, Frantisek; Hedegaard, Jakob; Nordentoft, Iver Kristiansen; Ørntoft, Torben Falck; Lund, Anders; Pedersen, Jakob Skou.

In: RNA, Vol. 20, No. 2, 20.02.2014, p. 236-251.

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Author

Nielsen, Morten Muhlig ; Theler, Disa ; Vang, Søren ; Sudzina, Frantisek ; Hedegaard, Jakob ; Nordentoft, Iver Kristiansen ; Ørntoft, Torben Falck ; Lund, Anders ; Pedersen, Jakob Skou. / Identification of expressed and conserved human noncoding RNAs. In: RNA. 2014 ; Vol. 20, No. 2. pp. 236-251.

Bibtex

@article{8a2bed54fe0742b193d925ecfcc49eea,
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. ",
author = "Nielsen, {Morten Muhlig} and Disa Theler and S{\o}ren Vang and Frantisek Sudzina and Jakob Hedegaard and Nordentoft, {Iver Kristiansen} and {\O}rntoft, {Torben Falck} and Anders Lund and Pedersen, {Jakob Skou}",
year = "2014",
month = feb,
day = "20",
doi = "10.1261/rna.038927.113",
language = "English",
volume = "20",
pages = "236--251",
journal = "RNA",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "2",

}

RIS

TY - JOUR

T1 - Identification of expressed and conserved human noncoding RNAs

AU - Nielsen, Morten Muhlig

AU - Theler, Disa

AU - Vang, Søren

AU - Sudzina, Frantisek

AU - Hedegaard, Jakob

AU - Nordentoft, Iver Kristiansen

AU - Ørntoft, Torben Falck

AU - Lund, Anders

AU - Pedersen, Jakob Skou

PY - 2014/2/20

Y1 - 2014/2/20

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.

U2 - 10.1261/rna.038927.113

DO - 10.1261/rna.038927.113

M3 - Journal article

C2 - 24344320

VL - 20

SP - 236

EP - 251

JO - RNA

JF - RNA

SN - 1355-8382

IS - 2

ER -