TY  - JOUR
A1  - Reid, Jeffrey G.
A1  - Nagaraja, Ankur K.
A1  - Lynn, Francis C.
A1  - Drabek, Rafal B.
A1  - Muzny, Donna M.
A1  - Shaw, Chad A.
A1  - Weiss, Michelle K.
A1  - Naghavi, Arash O.
A1  - Khan, Mahjabeen
A1  - Zhu, Huifeng
A1  - Tennakoon, Jayantha
A1  - Gunaratne, Gemunu H.
A1  - Corry, David B.
A1  - Miller, Jonathan
A1  - McManus, Michael T.
A1  - German, Michael S.
A1  - Gibbs, Richard A.
A1  - Matzuk, Martin M.
A1  - Gunaratne, Preethi H.
T1  - 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
Y1  - 2008/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1571 
EP  - 1581 
DO  - 10.1101/gr.078246.108 
VL  - 18 
IS  - 10 
UR  - http://genome.cshlp.org/content/18/10/1571.abstract 
N2  - Massively parallel sequencing of millions of <30-nt RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (βTC-3) reveals that ∼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. 
ER  -