Abstract
BackgroundThe Microprocessor, containing the RNA binding protein Dgcr8 and RNase III enzyme Drosha, is responsible for processing primary microRNAs to precursor microRNAs. The Microprocessor regulates its own levels by cleaving hairpins in the 5′UTR and coding region of the Dgcr8 mRNA, thereby destabilizing the mature transcript.Methodology/Principal FindingsTo determine whether the Microprocessor has a broader role in directly regulating other coding mRNA levels, we integrated results from expression profiling and ultra high-throughput deep sequencing of small RNAs. Expression analysis of mRNAs in wild-type, Dgcr8 knockout, and Dicer knockout mouse embryonic stem (ES) cells uncovered mRNAs that were specifically upregulated in the Dgcr8 null background. A number of these transcripts had evolutionarily conserved predicted hairpin targets for the Microprocessor. However, analysis of deep sequencing data of 18 to 200nt small RNAs in mouse ES, HeLa, and HepG2 indicates that exonic sequence reads that map in a pattern consistent with Microprocessor activity are unique to Dgcr8.Conclusion/SignificanceWe conclude that the Microprocessor's role in directly destabilizing coding mRNAs is likely specifically targeted to Dgcr8 itself, suggesting a specialized cellular mechanism for gene auto-regulation.
Highlights
MicroRNA maturation involves two processing steps [1]
To further test whether there is a broader role of the Microprocessor in the direct regulation of mRNAs, we evaluated the mRNA and small non-coding RNA profiles of wild-type, Dgcr8 KO and Dicer KO cells as well as a recently published data set of small RNAs less than 200 nucleotides from human Hela and HepG2 cell lines [17]
Similar to previous studies [14,18], we found multiple mRNAs whose expression were altered in cells that lacked Dgcr8
Summary
A long primary miRNA (pri-miRNA) is cleaved by the Microprocessor, containing the RNA binding protein Dgcr and the RNAseIII enzyme Drosha, to produce a 60–75 nucleotide hairpin precursor miRNA (pre-miRNA) in the nucleus [2,3,4,5,6]. Dicer processes endogenous siRNAs in mouse oocytes [11,12] Consistent with these additional roles of Dicer, Dgcr knockout (KO) ES cells have less severe phenotypes than Dicer knockout ES cells [13]. The Microprocessor, containing the RNA binding protein Dgcr and RNase III enzyme Drosha, is responsible for processing primary microRNAs to precursor microRNAs. The Microprocessor regulates its own levels by cleaving hairpins in the 59UTR and coding region of the Dgcr mRNA, thereby destabilizing the mature transcript
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