Limited evidence for evolutionarily conserved targeting of long non-coding RNAs by microRNAs
Babak Alaei-Mahabadi1, Erik Larsson
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden. erik.larsson@gu.se.
Silence
|August 22, 2013
Summary
Researchers investigated conserved microRNA targeting of long non-coding RNAs (lncRNAs). While conserved microRNA-mRNA interactions are common, conserved microRNA-lncRNA targeting was not reliably detected using comparative genomics.
Area of Science:
- Genomics
- Molecular Biology
- RNA Biology
Background:
- Long non-coding RNAs (lncRNAs) are key regulators of cell functions.
- The extent of microRNA targeting evolution in lncRNAs remains largely unexplored.
- Comparative genomics has identified conserved microRNA targeting in protein-coding mRNAs.
Purpose of the Study:
- To investigate the evolutionary conservation of microRNA target sites in lncRNAs.
- To compare microRNA targeting conservation between lncRNAs and mRNAs.
Main Methods:
- Utilized a map of predicted microRNA target sites in lncRNAs.
- Evaluated site conservation across 46 vertebrate species.
- Compared observed target site frequencies against a random model.
Main Results:
- Conserved microRNA target sites were generally not found above random expectation in intergenic lncRNAs.
- A small subset of cytoplasmic lncRNAs showed marginal over-representation of highly conserved 8-mer sites.
- The methodology efficiently detected conserved microRNA-mRNA targeting but yielded limited support for lncRNA interactions.
Conclusions:
- Evolutionary conservation of lncRNAs is typically low but can be high in specific regions.
- Conserved microRNA-lncRNA interactions could not be reliably detected with the applied methodology.
- Further research may be needed to develop robust methods for identifying conserved microRNA-lncRNA interactions.
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