The long non-coding RNA ACHLYS modulate biological condensates to regulate alternative splicing in root development

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 spliceosomal regulation and the transcriptome output in eukaryotic organogenesis.