Growing evidence supports the existence of a cross-talk between different post-transcriptional processes in regulating gene expression however, functional links between these processes and mechanisms of their interactions are not well understood. Alternatively spliced transcripts differ by intracellular localization, sensitivity to different RNA degradation machineries, such as RNA interference (RNAi) and nonsense-mediated mRNA decay (NMD), and protein-coding potential ( 8, 9). Up to 95% of human and 70% of plant multi-exonic genes are alternatively spliced producing from two to thousands of transcript variants per gene ( 3–7). Among them, alternative splicing, a process of differentially combining exons and introns or their parts to generate multiple mRNA isoforms from a single gene, significantly expands the transcriptomic landscape of eukaryotic cells ( 1, 2). Several post-transcriptional processes jointly orchestrate gene expression at the RNA level. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. However, its interactions with alternative splicing are poorly understood. RNA interference (RNAi) is a potent mechanism to modulate gene expression.
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD).
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