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Cell Rep. 2014 Apr 10;7(1):281-92. doi: 10.1016/j.celrep.2014.03.001. Epub 2014 Mar 20.

Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts.

Author information

1
Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA.
2
Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biology, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA. Electronic address: st2744@columbia.edu.

Abstract

Posttranscriptional regulatory programs governing diverse aspects of RNA biology remain largely uncharacterized. Understanding the functional roles of RNA cis-regulatory elements is essential for decoding complex programs that underlie the dynamic regulation of transcript stability, splicing, localization, and translation. Here, we describe a combined experimental/computational technology to reveal a catalog of functional regulatory elements embedded in 3' UTRs of human transcripts. We used a bidirectional reporter system coupled with flow cytometry and high-throughput sequencing to measure the effect of short, noncoding, vertebrate-conserved RNA sequences on transcript stability and translation. Information-theoretic motif analysis of the resulting sequence-to-gene-expression mapping revealed linear and structural RNA cis-regulatory elements that positively and negatively modulate the posttranscriptional fates of human transcripts. This combined experimental/computational strategy can be used to systematically characterize the vast landscape of posttranscriptional regulatory elements controlling physiological and pathological cellular state transitions.

PMID:
24656821
PMCID:
PMC4430845
DOI:
10.1016/j.celrep.2014.03.001
[Indexed for MEDLINE]
Free PMC Article

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