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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 direction of protein-coding genes often positively correlates with and is required for the expression 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  transcription and 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.

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