Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

We identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. Overall design: TSS-Seq was used to map the transcription initiation sites with single base resolution in A.thaliana seedlings (Col-0 with or without cold treatment);