Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Mercer, Tim R., Dinger, Marcel E., Bracken, Cameron P., Kolle, Gabriel, Szubert, Jan M., Korbie, Darren J., Askarian-Amiri, Marjan E., Gardiner, Brooke B., Goodall, Gregory J., Grimmond, Sean M. and Mattick, John S. (2010) Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Research, 20 12: 1639-1650. doi:10.1101/gr.112128.110

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Author Mercer, Tim R.
Dinger, Marcel E.
Bracken, Cameron P.
Kolle, Gabriel
Szubert, Jan M.
Korbie, Darren J.
Askarian-Amiri, Marjan E.
Gardiner, Brooke B.
Goodall, Gregory J.
Grimmond, Sean M.
Mattick, John S.
Title Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2010-12
Sub-type Article (original research)
DOI 10.1101/gr.112128.110
Open Access Status File (Publisher version)
Volume 20
Issue 12
Start page 1639
End page 1650
Total pages 12
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Collection year 2011
Language eng
Formatted abstract
The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5′ capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.
© 2010 by Cold Spring Harbor Laboratory Press

Keyword Messenger-RNA
Wide analysis
Start sites
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 36 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 42 times in Scopus Article | Citations
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Created: Sun, 19 Dec 2010, 00:13:37 EST