%0 Journal Article %J Genome Res %D 2008 %T 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. %A Reid, Jeffrey G %A Nagaraja, Ankur K %A Lynn, Francis C %A Drabek, Rafal B %A Muzny, Donna M %A Shaw, Chad A %A Weiss, Michelle K %A Naghavi, Arash O %A Khan, Mahjabeen %A Zhu, Huifeng %A Tennakoon, Jayantha %A Gunaratne, Gemunu H %A Corry, David B %A Miller, Jonathan %A McManus, Michael T %A German, Michael S %A Gibbs, Richard A %A Matzuk, Martin M %A Gunaratne, Preethi H %K Animals %K Base Sequence %K Cells, Cultured %K Deoxyuracil Nucleotides %K Embryo, Mammalian %K Female %K Mice %K MicroRNAs %K Molecular Sequence Data %K Nucleic Acid Conformation %K RNA Editing %K RNA Nucleotidyltransferases %K RNA Stability %K RNA, Messenger %K RNA, Small Untranslated %X

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.

%B Genome Res %V 18 %P 1571-81 %8 2008 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/18614752?dopt=Abstract %R 10.1101/gr.078246.108