The long non-coding RNA ACHLYS modulates biomolecular condensates to regulate alternative splicing in root development

Abstract

Alternative splicing (AS) enables eukaryotes to dynamically adjust RNA and protein isoforms encoded in one gene. Long non-coding RNAs (lncRNA) have emerged as novel regulators of AS through multiple modes of action, including interactions with splicing factor (SF) proteins. Here, we used Arabidopsis thaliana lateral root development to dissect the specificity of lncRNAs in AS regulation. Data mining and a transient expression screen allowed us to identify novel lncRNAs interacting in vivo with the well-characterized SFs Nuclear speckle RNA binding protein A (NSRa) and glycine-rich RNA-binding protein 7 (GRP7), that are differentially expressed during lateral root organogenesis. We identified 4 lncRNAs affecting more than 250 AS events in plant cells, whereby most AS events are unique for each lncRNA. Notably, 19% of the AS events linked to two NSRa-recognized lncRNAs are identical and positively correlated. One lncRNA was named ACHLYS and is highly conserved in several Brassicaceae whereas another was the recently characterized FLAIL lncRNA. ACHLYS knockdown (KD-ACHLYS) and overexpressing lines (OE-ACHLYS) modulate AS regulation in plants and affect root architecture. In parallel, we performed NSRa-iCLIP to determine in vivo genome-wide NSRa binding sites. Interestingly, NSRa binding sites are locally enriched in ACHLYS-dependent AS introns and ACHLYS itself. A specific ACHLYS-induced AS event requires NSRa function showing that ACHLYS defines AS targets through NSRa interaction on specific transcripts. In vitro assays indicate that direct interaction of NSRa with ACHLYS promotes NSRa phase separation. Furthermore, overexpression of ACHLYS in NSRa-GFP plants results in increased accumulation of NSRa in Nuclear speckles. Our data revealed that ACHLYS can modulate NSRa condensates in vivo and binds to NSRa for modifying AS patterns, suggesting a new mechanism where lncRNAs can fine tune SFs regulation and the transcriptome output in eukaryotic organogenesis.