Fig. 1

Transcription Start Site (TSS) sequencing in Col-0 after 3 h of exposure to 4 °C identified the long non-coding RNA, SVALKA. a Differentially expressed TSS after cold exposure in Col-0. A total of 1893 TSS changed their expression significantly (p < 0.05). Of these, 489 were down-regulated while 1404 were up-regulated. The TSS were classified according to their position relative to  gene bodies . The majority of differentially expressed TSS were found in or around promoters. b Activity of up-regulated promoters after cold exposure identities the CBF genes (indicated in blue bars) as highly up-regulated. Graph represents the fold change of the top 25 up-regulated promoters in Col-0 after cold exposure. c Screenshot of the CBF genomic region and the identified TSS. The upper panel shows the sense TSS-seq reads direction (blue) and clear TSS can be found for the three CBF genes. The lower panel shows the TSS-seq reads in antisense direction (orange) where a group of cold-induced TSS was identified in the intergenic region between CBF1 and CBF3. d Summary of 3′- and 5′-RACE of SVALKA. Two clusters of capped TSS were found for SVALKA, a distal TSS centered around 2360 bp and a proximal TSS centered around 1386 bp in respect to the translation start of CBF1. A cluster of polyadenylation sites were found 846–897 bp in respect to the translation start of CBF1. The plethora of SVALKA transcripts includes a spliced isoform with a splice site from 1386 to 2113 bp in respect to the translation start of CBF1. e RNA levels of CBF1 and SVALKA during a time course of cold exposure of Col-0. While CBF1 transiently is upregulated early in the cold response, SVALKA responds later and its expression is anti-correlated to sense CBF1. UBI is used as a loading control. Experiments were done with three biological replicates showing similar results. Uncropped blots can be found in the Source Data file