Shade‐induced lncRNAPUAR promotes shade response by repressing PHYA expression

Abstract Shade avoidance syndrome (SAS) commonly occurs in plants experiencing vegetative shade, triggering a series of morphological and physiological changes for the plants to reach more light. A number of positive regulators, such as PHYTOCHROME‐INTERACTING 7 (PIF7), and negative regulators, such as PHYTOCHROMES, are known to ensure appropriate SAS. Here, we identify 211 shade‐regulated long non‐coding RNAs (lncRNAs) in Arabidopsis . We further characterize PUAR ( PHYA UTR Antisense RNA), a lncRNA produced from the intron of the 5′ UTR of the PHYTOCHROME A ( PHYA ) locus. PUAR is induced by shade and promotes shade‐induced hypocotyl elongation. PUAR physically associates with PIF7 and represses the shade‐mediated induction of PHYA by blocking the binding of PIF7 to the 5′ UTR of PHYA . Our findings highlight a role for lncRNAs in SAS and provide insight into the mechanism of PUAR in regulating PHYA gene expression and SAS.