Drosha and Dicer are the RNase III enzymes that responsible for microRNA (miRNA) biogenesis in animals. They function consecutively, with Drosha in the nucleus first cleaving the long primary (pri-)miRNA transcript. This releases a hairpin pre-miRNA intermediate. In the cytoplasm, Dicer subsequently cleaves the hairpin ~22nt from Drosha cleavage site, releasing a miRNA duplex. One strand becomes the mature miRNA to guide the RNA-induced silencing complex (RISC) to mRNAs. Recognition of complementary sequences in target mRNAs results in post-transcriptional repression.
We and others discovered that Drosha can also regulate mRNAs by direct cleavage, independent of its role in miRNA biogenesis. These mRNAs appear to harbour stem-loop structures that resemble pri-miRNAs. Interestingly, most of Drosha direct cleavage targets are only found in the pluripotent cells. In this study, we used high throughput Degradome-sequencing of Drosha-deficient embryonic stem cells in order to map direct cleavage targets. The stem-loop structures in mRNAs that are direct targets of Drosha appear to exhibit features that are slightly different compared to pri-miRNA stem-loops.
Dicer has also been reported to regulate the expression of other RNAs, independent of its role in miRNA biogenesis, such as retrotransposons. However, whether Dicer directly cleaves retrotransposon RNA is not clear. To address this, we therefore also performed Degradome-sequencing of Dicer deficient embryonic stem cells.