Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite directionof protein-coding genes often positively correlates with and is required for theexpression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus.MAS is induced by cold and indispensable for the activation of MAF4 transcriptionand suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes To globally identify lncRNAs in Arabidopsis, we reconstructed an Arabidopsis transcriptome using high depth strand-specific RNA sequencing (ssRNA-seq). We generated cDNA libraries for rRNA-depleted total, polyadenylated [poly(A)+] and non-polyadenylated [poly(A)-] RNAs in whole cell extract, nuclear and cytosolic fractions that were prepared from Arabidopsis grown under normal or stress conditions