ALTERNATIVE SPLICING OF A CODING GENE PRODUCES A NUCLEAR REGULATORY LONG NON-CODING RNA

Summary Alternative splicing (AS) is traditionally understood to increase transcript and protein diversity by generating multiple coding isoforms from a single gene. In addition, many alternative isoforms are degraded through non-sense mediated decay (NMD). Furthermore, we show here that AS also produces nuclear long non-coding RNAs (lncRNAs) from protein-coding genes, which can serve regulatory functions rather than expanding proteomic complexity. Focusing on the Arabidopsis thaliana SR protein gene At-RS31 , we found that a non-coding isoform ( mRNA3 ) accumulates in the nucleus under dark conditions. This transcript binds the protein product of its own transcriptional unit, modulating splicing decisions and balancing gene activity in response to environmental cues. Overexpression of mRNA3 down-regulates the action of At-RS31 on its target genes in trans and restores the phenotype induced by intron-less At-RS31 accumulation. Further sub-cellular fractionation and RT-PCR analyses show that many SR genes generate nuclear-retained non-coding isoforms, especially under dark conditions, suggesting a widespread mechanism. These findings redefine the role of AS in plants, highlighting its capacity to generate regulatory lncRNAs to fine-tune gene expression beyond protein diversification. Highlights - Alternative splicing generates regulatory lncRNAs from protein-coding genes - A nuclear-retained isoform forms an autoregulatory RNA–protein feedback loop - Non-coding isoforms of SR genes accumulate in the nucleus under dark conditions - Co-expression of the non-coding isoform rescues splicing factor overexpression phenotypes