Coordinated regulation of developmental transition by protein and long noncoding RNA components Project Summary Epigenetic mechanisms enable organisms to adapt to developmental and environmental cues. Plants have evolved intricate regulatory networks to control development in response environmental stimuli such as temperature and light. For example, prolonged cold triggers vernalization, a process that accelerates flowering through epigenetic changes in genes involved in development. Therefore, the vernalization response in Arabidopsis is an excellent model system for study of complex epigenetic regulation of gene expression triggered by environmental cues in eukaryotes. Vernalization-mediated epigenetic changes include the formation of chromatin loops and alterations in chromatin modifications and in expression of long noncoding RNAs (lncRNAs). Changes in the three-dimensional structure of the genome, such as formation of local chromatin loops, are increasingly recognized as important gene regulatory events in eukaryotes; however, how chromatin modifications and lncRNAs coordinate to influence gene expression through changes in the three-dimensional structure of the genome is not well understood. Here we seek to understand the mechanistic details of how the three-dimensional structure of the genome influences gene regulation in vivo using developmental changes in flowering and photomorphogenesis as phenotypical read- outs. Our overriding goal is to elucidate structural and regulatory components governing protein- and lncRNA-mediated epigenetic gene regulation in Arabidopsis through three specific aims designed to: 1) elucidate the detailed mechanisms of chromatin structure-mediated gene regulation focusing on two groups of chromatin architectural proteins that we showed coordinate gene regulation through the formation of chromatin loops, 2) characterize mechanisms underlying light signaling-mediated chromatin conformation changes, and 3) characterize genome-wide changes in chromatin structure induced by environmental stimuli. Our approach will reveal the mechanistic details of chromatin structure-based epigenetic regulation by both protein and lncRNA components during flowering and photomorphogenesis. These findings will further our understanding of the mechanism of epigenetic regulation of gene expression, which has a deep evolutionary root among eukaryotes.