Long noncoding RNAs (lncRNAs) are emerging as key regulators of plant development, yet their nuclear-specific roles remain poorly understood. Previously, we demonstrated key roles for several transposonable associated lncRNAs, TE-lincRNAs, under salt and drought stress in Arabidopsis thaliana (1). Using the INTACT (Isolation of Nuclei TAgged in specific Cell Types) method combined with deep stranded Illumina RNA-sequencing from A. thaliana endosperm nuclei, we identified about >20,000 lncRNAs (2,3). One nuclear-enriched antisense lncRNA which we designate NAOS1 (Nuclear Antisense Organ Size 1) that is not polyadenylated, is highly abundant in nuclear RNA fractions but absent from the cytoplasm, consistent with a nuclear regulatory function.
T-DNA and CRISPR-Cas9-induced knockouts of NAOS1 results in plants with significantly reduced cell and organ size, including smaller leaves, roots, and floral organs and seeds. Histological analyses confirmed that these phenotypes are due to reduced cell expansion, not cell number. Notably, NAOS1 is deeply conserved and is detected in Marchantia polymorpha, and higher plants Oryza sativa(rice), Brassica rapa, and A. alpina, indicating an evolutionarily conserved role for this lncRNA family in growth regulation.
Complementation of the naos1 mutant with a wild-type NAOS1 transgene under its native or strong CaMV35S promoters fully restores normal organ and cell size, and this rescue is observed in trans, suggesting that NAOS1 functions as a diffusible regulator within the nucleus. Our findings uncover a deeply conserved, nuclear-resident lncRNA that regulates plant organogenesis through modulation of cell size and highlights the potential for antisense lncRNAs to act as trans-acting developmental regulators in plants.