The authors examined how the long non-coding RNAs SVALKA (SVK) and SVALNA (SVN) regulate the cold‑responsive transcription factors CBF1 and CBF3 in Arabidopsis thaliana. Using native elongation transcript sequencing, CRISPR‑Cas9 deletions, and RT‑qPCR, they showed that SVK acts both in cis and trans through RNAPII collision and chromatin remodeling, while SVN acts cis‑negatively via RNAPII collision, with isoform diversity generated by alternative splicing being critical for function.