Optimal timing of flowering is of central importance to plant fitness, in both ecological and agricultural contexts. Plants integrate a variety of cues to determine the right time to flower; for many species, this includes an obligate requirement for the long period of cold experienced over winter (vernalization). In the face of an increasingly warm and variable climate, clarifying the mechanism of cold signal integration in determining flowering is of high importance.
In the model plant Arabidopsis thaliana, the integration of cold as a flowering signal is controlled by the flowering repressor gene FLOWERING LOCUS C (FLC). During winter, prolonged cold quantitatively down-regulates FLC expression across the whole plant, acting via an “ON/OFF” epigenetic switch at the level of the single cell. A long non-coding RNA, COOLAIR, is transcribed antisense to FLC and plays a key role in this switching mechanism. Plants in which COOLAIR transcription has been blocked show slower silencing of FLC in the cold and altered epigenetic switching dynamics. Like many non-coding RNAs in other systems, COOLAIR RNA can form folded secondary structures in in vitro systems that seem to be conserved across related species. This folding may be functionally important to the silencing of FLC in winter, perhaps by recruiting proteins known to be involved in the epigenetic switch.
Here, plants with slightly altered COOLAIR sequences were produced with the intention of disrupting their folded structures. Some of the alterations generated plants with late flowering and atypical patterns of FLC silencing in cold, suggesting a functional role for the folded structure. In parallel, ongoing work in the Dean lab and collaborators, methods were developed for determining the folded structures of COOLAIR in planta, and for identifying proteins that associate with the RNA during vernalization.
