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.
Bibliographical noteFunding Information:
The FLAG-Drosha plasmid and the FLAG-DGCR8 plasmid were kind gifts from Dr. V. Narry Kim (Seoul University). The AGO2 plasmid was kindly provided by Dr. Sven Diederichs (German Cancer Research Center [DKFZ]). We thank Dr. Noam Shomron and Dr. Schraga Schwartz and for comments and critical reading of the manuscript. We thank Mr. Dror Hollander for valuable input into this study. We thank Dr. Rani Elkon for statistical advice. G.A. and S.K. were supported by a grant from the Israel Science Foundation (ISF-BIkura 838/10). G.A. was funded by grants from the Israel Science Foundation (ISF) (ISF 61/09), ISF-Morasha 64/12, the Israel Cancer Association, and the Israel Cancer Research Foundation. S.K. was supported by ISF 1015/10 and a Marie Curie International Reintegration Grant. A.L. is grateful to the Azrieli Foundation for the award of an Azrieli Fellowship. N.A. was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. R.S. was supported by a research grant from the ISF (Grant No. 241/11). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.