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

• Published in: Molecular cell 2013-06, Vol.50 (6), p.869-881
• Main Authors: Melamed, Ze’ev, Levy, Asaf, Ashwal-Fluss, Reut, Lev-Maor, Galit, Mekahel, Keren, Atias, Nir, Gilad, Shlomit, Sharan, Roded, Levy, Carmit, Kadener, Sebastian, Ast, Gil
• Format: Article
• Language: English
• Subjects: Alternative Splicing; Animals; Base Sequence; biogenesis; cell death; Cell Death - genetics; Exons; Gene Regulatory Networks; HEK293 Cells; High-Throughput Nucleotide Sequencing; Humans; Introns; Inverted Repeat Sequences; Mice; microRNA; MicroRNAs - biosynthesis; MicroRNAs - genetics; Molecular Sequence Data; Multigene Family; neurons; Neurons - physiology; Nucleic Acid Conformation; Proteins - metabolism; Ribonuclease III - genetics; Ribonuclease III - metabolism; RNA Interference; RNA Splice Sites; RNA-Binding Proteins
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2013.05.007

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. [Display omitted] •Alternative splicing directly affects biogenesis of splice-site-overlapping miRNAs•Levels of DGCR8/Drosha modulate inclusion level of exons that overlap pre-miRNAs•Levels of mRNA targets of such miRNA are correlated with exon inclusion in vivo•The Microprocessor and the spliceosome compete for processing of the same RNA loci