AnArabidopsislong noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

Abstract

ABSTRACTAlternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. InArabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with theALTERNATIVE SPLICING COMPETITOR (ASCO)lncRNA. Here, we analyzed the effect of the knockdown and overexpression ofASCOat genome-wide level and found a high number of deregulated and differentially spliced genes, related to flagellin responses and biotic stress. In agreement, roots fromASCO-knocked down plants are more sensitive to flagellin. Surprisingly, only a minor subset of genes overlapped with the AS defects of thensra/bdouble mutant. Using biotin-labelled oligonucleotides for RNA-mediated ribonucleoprotein purification, we found thatASCObinds to the highly conserved core spliceosome component PRP8a.ASCOderegulation impairs the recognition of specific flagellin-related transcripts by PRP8a and SmD1b, another spliceosome component, suggesting thatASCOfunction regulates AS through the interaction with multiple splicing factors. Hence, lncRNAs may interact in a dynamic network with many splicing factors to modulate transcriptome reprogramming in eukaryotes.