We have sequenced miRNA libraries from human embryonic,
neural and foetal mesenchymal stem cells.
We report that the majority of miRNA genes encode
mature isomers that vary in size by one or
more bases at the 3 and/or 5 end of the miRNA.
Northern blotting for individual miRNAs showed that
the proportions of isomiRs expressed by a single
miRNA gene often differ between cell and tissue
types. IsomiRs were readily co-immunoprecipitated
with Argonaute proteins in vivo and were active in
luciferase assays, indicating that they are functional.
Bioinformatics analysis predicts substantial differences
in targeting between miRNAs with minor 5
differences and in support of this we report that a 5
isomiR-9–1 gained the ability to inhibit the expression
of DNMT3B and NCAM2 but lost the ability to
inhibit CDH1 in vitro. This result was confirmed by
the use of isomiR-specific sponges. Our analysis of
the miRGator database indicates that a small percentage
of human miRNA genes express isomiRs as
the dominant transcript in certain cell types and analysis
of miRBase shows that 5 isomiRs have replaced
canonical miRNAs many times during evolution. This
strongly indicates that isomiRs are of functional importance
and have contributed to the evolution of
miRNA genes.
INT