An antisense RNA forms R-loop to facilitate the transcription of CBF genes and plant cold acclimation

Cold acclimation is an adaption used by many plants to survive freezing temperatures and involves rapid induction of the expression of three C-REPEAT-BINDING FACTOR (CBF) genes. We have previously annotated long non-coding RNAs (lncRNAs) including natural antisense transcripts (NAT-lncRNAs) on a genome-wide scale in Arabidopsis and identified a NAT-lncRNA transcribed from the antisense strand between CBF1 and CBF3. We named it CAS for CBF antisense transcript. CAS corresponds to two of the three β isoforms of the lncRNA SVALKA (SVK) previously reported. We show that CAS/SVK is induced to a high level shortly after cold exposure and positively controls CBF1 and CBF3 expression during acclimation, which in turn confers acquired freezing tolerance of plants. CAS/SVK organizes an R-loop to reduce nucleosome occupancy, thus facilitating CBF1 and CBF3 transcription. Our study demonstrates a distinct role of CAS/SVK in facilitating neighboring gene transcription and underscores the importance of lncRNA-mediated control in cold acclimation.