Impact of alternative splicing on Arabidopsis thaliana. Splicing factors and the role of non-coding isoforms

LUCAS SERVI; FLORENCIA SOL RODRIGUEZ; NICOLÁS BELLORA; EZEQUIEL PETRILLO

Santa Fe

Congreso; RAFV Conference 2021. XXXIII Argentinian meeting of Plant Physiology; 2021

Light signals induce a massive reprogramming of gene expression in plants. Alternative splicing (AS) produces multiple mRNAs (variants or isoforms) from a single gene through the variable, and regulated, choice of different splicing sites. In addition to generating several isoforms that can be translated into different proteins, this process can also give rise to variants without coding capacity, allowing a fine control of protein levels. The non-coding AS-derived isoforms could be also acting as long non-coding RNAs (lncRNAs). These  regulatory RNAs can control chromatin status, modulate the abundance of other RNAs, and affect translation. Light regulates the AS in A. thaliana, including the gene At-RS31. Changes in the splicing patterns of this gene modulate the amount of protein generated (splicing factor), since only one isoform is translatable, mRNA1. Although the overexpression of mRNA1 generates deleterious phenotypes, by overexpressing all the variants (genomic construction), the resulting plants present normal phenotypes. We previously demonstrated that the other predominant isoform of At-RS31, mRNA3, is retained in the nucleus. These findings invited us to hypothesize that this transcript could be fulfilling a nuclear regulatory function, being a lncRNA generated by AS. This reasoning led to the bioinformatics search for other potential transcripts showing similar characteristics. For this, the differential expression of the isoforms of A. thaliana was analyzed in multiple RNAseq (from public repositories) linked to RNA translation, degradation, and localization. As a result of this analysis, we found numerous novel candidates, which resemble the At-RS31 mRNA3 and could function as lncRNAs in Arabidopsis.