Pan aims to understand of how secondary structure of an antisense transcript COOLAIR can functionally influence the chromatin environment and expression of the sense coding gene FLC, which is a central player in determining the timing of the switch to reproduction.
Antisense noncoding RNAs are pervasively expressed in eukaryotes and are now being recognized as having important roles in biological processes. Many of these non-coding transcripts have conserved secondary structure, despite low conservation of primary sequence, suggesting an important connection between structure and function. COOLAIR has been shown to mediate the transcriptional silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC), a crucial repressor of the transition to flowering.
The spliced form can fold into a complex secondary structure in vitro which is evolutionarily conserved throughout the Brassicaceae, despite low sequence identity. Pan is focusing on the in vivo secondary structure of COOLAIR, which may change at different temperatures thus influencing the transcriptional state of FLC.
Pan is also interested in a recently discovered natural variant of Arabidopsis COOLAIR with changed secondary structure and will study how this single natural polymorphism functionally influences FLC transcription.