Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes.

TitleMouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes.
Publication TypeJournal Article
Year of Publication2008
AuthorsReid, JG, Nagaraja, AK, Lynn, FC, Drabek, RB, Muzny, DM, Shaw, CA, Weiss, MK, Naghavi, AO, Khan, M, Zhu, H, Tennakoon, J, Gunaratne, GH, Corry, DB, Miller, J, McManus, MT, German, MS, Gibbs, RA, Matzuk, MM, Gunaratne, PH
JournalGenome Res
Volume18
Issue10
Pagination1571-81
Date Published2008 Oct
ISSN1088-9051
KeywordsAnimals, Base Sequence, Cells, Cultured, Deoxyuracil Nucleotides, Embryo, Mammalian, Female, Mice, MicroRNAs, Molecular Sequence Data, Nucleic Acid Conformation, RNA Editing, RNA Nucleotidyltransferases, RNA Stability, RNA, Guide, RNA, Messenger
Abstract

Massively parallel sequencing of millions of < 30-nt RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (betaTC-3) reveals that approximately 50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences. Approximately, 12%-20% of species associated with mmu-let-7 populations exhibit sequence discrepancies that are dramatically reduced in nucleotides 3-7 (5'-seed) and 10-15 (cleavage and anchor sites). This observation is inconsistent with sequencing error and leads us to propose that the changes arise predominantly from post-transcriptional RNA-editing activity operating on miRNA:target mRNA complexes. Internal nucleotide modifications are most enriched at the ninth nucleotide position. A common ninth base edit of U-to-G results in a significant increase in stability of down-regulated let-7a targets in inhibin-deficient mice (Inha-/-). An excess of U-insertions (14.8%) over U-deletions (1.5%) and the presence of cleaved intermediates suggest that a mammalian TUTase (terminal uridylyl transferase) mediated dUTP-dependent U-insertion/U-deletion cycle may be a possible mechanism. We speculate that mRNA target site-directed editing of mmu-let-7a duplex-bulges stabilizes "loose" miRNA:mRNA target associations and functions to expand the target repertoire and/or enhance mRNA decay over translational repression. Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies ("intranomics") can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs.

DOI10.1101/gr.078246.108
Alternate JournalGenome Res.
PubMed ID18614752
PubMed Central IDPMC2556275
Grant ListR01 DK021344 / DK / NIDDK NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
2 U54 HG003273-4 / HG / NHGRI NIH HHS / United States
R01DK21344 / DK / NIDDK NIH HHS / United States