Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions

Abstract

The initial step in microRNA (miRNA) biogenesis requires processing of the precursor miRNA (pre-miRNA) from a longer primary transcript. Many pre-miRNAs originate from introns, and both a mature miRNA and a spliced RNA can be generated from the same transcription unit. We have identified a mechanism in which RNA splicing negatively regulates the processing of pre-miRNAs that overlap exon-intron junctions. Computational analysis identified dozens of such pre-miRNAs, and experimental validation demonstrated competitive interaction between the Microprocessor complex and the splicing machinery. Tissue-specific alternative splicing regulates maturation of one such miRNA, miR-412, resulting in effects on its targets that code a protein network involved in neuronal cell death processes. This mode of regulation specifically controls maturation of splice-site-overlapping pre-miRNAs but not pre-miRNAs located completely within introns or exons of the same transcript. Our data present a biological role of alternative splicing in regulation of miRNA biogenesis.

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

“…These results indicate that expression of these apparently linked miRNAs may be uncoupled in some settings. Finally, our data confirm previous analyses that identified miRNAs that span splice sites (Melamed et al 2013), supporting a role for alternative splicing in regulating the expression of specific miRNAs.…”

“…A previous analysis of existing expressed sequence tags (ESTs) and mRNAs revealed a class of pre-miRNA sequences that span intronexon junctions such that splicing prevents processing of these miRNA hairpins by the microprocessor complex (Melamed et al 2013). We were able to confirm the existence of pri-miRNAs with this configuration using our assemblies (Supplemental Table S4).…”

microRNAs are biomarkers of oncogenic human papillomavirus infections

“…Our data indicate that the expression of oncogenic miRNAs is superimposed over that of the tumor-suppressive miRNAs as a net gain by HR HPV infection. It is possible that the posttranscriptional regulation could also play a role in this net gain, because p53 interacts with Drosha/p68 complex to facilitate Drosha-mediated primarymiRNA processing of certain miRNAs (27) and some miRNAs derived from intron regions are coupled to RNA splicing (59,60).…”

Epithelial Splicing Regulatory Proteins 1 (ESRP1) and 2 (ESRP2) Suppress Cancer Cell Motility via Different Mechanisms

“…It is thus possible that ESRP2 suppresses ␦EF1 and SIP1 by regulating miRNA expression. Melamed et al (37) recently reported that the alternative splicing machinery competes with the miRNA processing machinery when a pre-miRNA sequence overlaps with active splice sites. However, EMT-associated pre-miRNA sequences (miR-34, miR-200 family, and miR-9) do not overlap exon-intron junctions, ruling out such a mechanism.…”