Abstract
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.
Highlights
Long non-coding RNAs have emerged as important regulators of gene expression and plant development
We identified a large number of Long non-coding RNAs (lncRNAs) and analyzed their expression profile in different tissues under normal or stress conditions using strandspecific RNA sequencing (RNA-seq)
The lncRNAs we identified represent a valuable addition to the Arabidopsis lncRNA collection, and provide a rich resource for the community to further investigate the biology of lncRNAs in plants
Summary
Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. 1234567890():,; Long non-coding RNAs (lncRNAs) have emerged as important players in the regulation of gene transcription, splicing, and translation[1,2]. Instead of being transcriptional regulators, ASCO-lncRNA was found to associate with the nuclear speckle RNA-binding protein (NSR) and modulate NSR-mediated alternative splicing events through mimicking and displacing pre-mRNA targets[37]. We further demonstrated that one NATlncRNA, MAS, positively regulates the transcription of its cognate sense gene MAF4 through interacting with and recruiting WDR5a, a core component of the COMPASS-like complexes, to MAF4, thereby regulating flowering time. Our study provides a resource for studying lncRNAs in Arabidopsis and reveals a mechanism for gene regulation by NAT-lncRNAs
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