Atrans-acting long non-coding RNA represses flowering inArabidopsis

Eukaryotic genomes give rise to thousands of long non-coding RNAs (lncRNAs), yet the purpose of lncRNAs remains largely enigmatic. Functional characterization of lncRNAs is challenging due to multiple orthogonal hypothesis for molecular activities of lncRNA loci. Here, we identified afloweringassociatedintergeniclncRNA (FLAIL) that represses flowering inArabidopsis. An allelic series offlailloss-of-function mutants generated by CRISPR/Cas9 and T-DNA mutagenesis showed an early flowering phenotype. Gene expression analyses inflailmutants revealed differentially expressed genes linked to the regulation of flowering. A genomic rescue fragment ofFLAILintroduced inflailmutants complemented gene expression defects and early flowering, consistent withtrans-acting effects of theFLAILRNA. Knock-down ofFLAILRNA levels using the artificial microRNA approach revealed an early flowering phenotype shared with genomic mutations, indicating atrans-acting role ofFLAILRNA in the repression of flowering time. Genome-wide detection ofFLAIL-DNA interactions by ChIRP-seq suggested thatFLAILmay directly bind genomic regions.FLAILbound to genes involved in regulation of flowering that were differentially expressed inflail, consistent with the interpretation ofFLAILas atrans-acting lncRNA directly shaping gene expression. Our findings highlightFLAILas atrans-acting lncRNA that affects flowering inArabidopsis, likely through mediating transcriptional regulation of genes directly bound byFLAIL.