Reexamining microRNA site accessibility in Drosophila: A population genomics study

Kevin Chen, Jonas Maaskola, Mark Siegal, Nikolaus Rajewsky

Research output: Contribution to journalArticle

Abstract

Kertesz et al. (Nature Genetics 2008) described PITA, a miRNA target prediction algorithm based on hybridization energy and site accessibility. In this note, we used a population genomics approach to reexamine their data and found that the PITA algorithm had lower specificity than methods based on evolutionary conservation at comparable levels of sensitivity. We also showed that deeply conserved miRNAs tend to have stronger hybridization energies to their targets than do other miRNAs. Although PITA had higher specificity in predicting targets than a naïve seed-match method, this signal was primarily due to the use of a single cutoff score for all miRNAs and to the observed correlation between conservation and hybridization energy. Overall, our results clarify the accuracy of different miRNA target prediction algorithms in Drosophila and the role of site accessibility in miRNA target prediction.

Original languageEnglish (US)
Article numbere5681
JournalPLoS One
Volume4
Issue number5
DOIs
StatePublished - May 25 2009

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Metagenomics
MicroRNAs
microRNA
Drosophila
hybridization
prediction
energy
Conservation
seeds
methodology
Seed
Genomics
Seeds

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Reexamining microRNA site accessibility in Drosophila : A population genomics study. / Chen, Kevin; Maaskola, Jonas; Siegal, Mark; Rajewsky, Nikolaus.

In: PLoS One, Vol. 4, No. 5, e5681, 25.05.2009.

Research output: Contribution to journalArticle

Chen, Kevin ; Maaskola, Jonas ; Siegal, Mark ; Rajewsky, Nikolaus. / Reexamining microRNA site accessibility in Drosophila : A population genomics study. In: PLoS One. 2009 ; Vol. 4, No. 5.
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