The non-coding RNA SVALKA locus produces a cis- natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures

Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism's ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in regulating coding transcription. However, the molecular insights into the regulation are largely unknown. Here, we show that a long isoform of the long non-coding RNA, SVALKA-L (SVK-L), forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action for SVK-L. This pathway includes the formation of double stranded RNA that is recognized by the DICER proteins and subsequent down-regulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for the previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes a developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady state levels of their host gene's mRNA.