Co-transcriptional splicing changes combine with reduced productive transcription initiation for cold-induced repression of <i>FLC</i>

The Arabidopsis floral repressor locus FLC is epigenetically silenced during winter cold to align flowering with spring. During weeks of cold exposure, FLC transcription is progressively reduced both by transcriptional repression mediated by FLC antisense transcription and epigenetic silencing implemented through a Polycomb-mediated epigenetic switch. In the warm, FLC is transcriptionally repressed by coordinated changes in transcription initiation and RNA PolII speed in a mechanism involving proximal termination. Whether similar mechanisms contribute to the cold-induced FLC transcriptional repression is unknown. Here, we combine mathematical modelling and transcription profiling to investigate FLC transcriptional changes during the cold. We find different dynamics of spliced and unspliced transcripts during cold exposure with only a small change in PolII speed. We also show that, unlike short-term cold, long-term cold temperatures drive an increase in splicing rates while simultaneously reducing productive transcription at FLC. This process is influenced by antisense COOLAIR transcription but does not rely on proximal COOLAIR termination. Cold-induced transcriptional repression of FLC thus involves a decoupling of changes in productive transcription initiation from PolII speed and rates of co-transcriptional splicing, a different mechanism from that repressing FLC in the warm.