PRMT1 regulates microRNA biogenesis through the methylation of the Large Drosha Complex

MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Large Drosha Complex (LDC). We previously reported that the LDC is highly methylated. To investigate the extent of this post-translational modification, we extensively characterized the LDC methyl-proteome by combining heavy methyl SILAC metabolic labelling of cells with the affinity-enrichment of the complex, followed by high resolution mass spectrometry (MS) analysis. We found that arginine (R) methylation is the predominant modification, occurring on multiple sites of 13 of the 23 subunits of the complex. Interestingly, the depletion- or pharmacological inhibition- of PRMT1, the major protein R-methyltransferase in mammals, alters the LDC methylation state and this is linked to a global decrease of miRNA expression, due to the specific impairment of the pri-to-pre-miRNA processing step. Moreover, PRMT1 activity appears to be required for the binding of some LDC subunits to pri-miRNAs. Overall, our study uncovers a previously uncharacterized role of R-methylation in the regulation of the LDC activity, thus effecting miRNA levels in mammalian cells Overall design: MicroRNA expression analysis by deep-sequencing in HeLa cells upon PRMT1 knock-down