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PMID: 21335607 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets.

Nucleic acids research ·Vol. 39 ·No. 11 ·2011-06-00 ·Pages 4827-35

Lambert NJ, Gu SG, Zahler AM

Abstract

MicroRNAs control gene expression by post-transcriptional down-regulation of their target mRNAs. Complementarity between the seed region (nucleotides 2-8) of a microRNA and the 3'-UTR of its target mRNA is the key determinant in recognition. However, the structural basis of the ability of the seed region to dominate target recognition in eukaryotic argonaute complexes has not been directly demonstrated. To better understand this problem, we performed chemical probing of microRNAs held in native argonaute-containing complexes isolated from Caenorhabditis elegans. Direct probing of the RNA backbone in isolated native microRNP complexes shows that the conformation of the seed region is uniquely constrained, while the rest of the microRNA structure is conformationally flexible. Probing the Watson-Crick edges of the bases shows that bases 2-4 are largely inaccessible to solvent, while seed region bases 5-8 are readily modified; collectively our probing results suggest a model in which these bases are primed for initiating base pairing with the target mRNA. In addition, an unusual DMS reactivity with U at position 6 is observed. We propose that interaction of miRNAs with argonaute proteins pre-organizes the structure of the seed sequence for specific recognition of target mRNAs.

MeSH Terms
Animals Base Pairing Caenorhabditis elegans/genetics Carbohydrates/chemistry DNA/chemistry,metabolism MicroRNAs/chemistry Nucleic Acid Conformation Phosphates/chemistry RNA, Messenger/chemistry Ribonucleoproteins/chemistry,metabolism
Chemicals
Carbohydrates MicroRNAs Phosphates RNA, Messenger Ribonucleoproteins DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Lambert Nicole J
Department of MCD Biology and the Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA.
Gu Sam G
Zahler Alan M
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkr077
Published
2011-06-00
Epub
2011-00-18
Pages
4827-35
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3113585
Subset
IM
Grants
NIGMS NIH HHS · R01 GM-0161646 · United States
External Links
PubMed source DOI: 10.1093/nar/gkr077 PMC Full Text View journal details
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