In plants, the environmental cue of light plays an essential role in proper growth and photosynthesis. The purpose of this study is to investigate the role and mechanism of nuclear organization in response to light signaling in the model organism Arabidopsis thaliana. We investigate whether light signaling regulates positioning and spatial orientation of light-induced genes and determine whether its transcriptional activation is dependent on its repositioning. The outcome of this study will enable us to further understand how reorganization of the genes translates to large-scale developmental changes in response to environmental cues. Our study will demonstrate a functional link between transcriptional regulation and nuclear organization by uncovering the mechanism of how light signaling regulators remodel single genes.

The theory that chromosomes occupy certain locations in the nucleus is described as the “chromosomal territory” theory, first characterized by Rabl in 1885. The advancement of technology in fluorescent in situ hybridization (FISH) methods confirmed this model and have become crucial in studying nuclear organization within eukaryotic systems. There has been increasing evidence that environmental cues influence the organization of chromatin and repositioning of genes. Due to the sessile nature of plants, they must adapt to their environment for better survival by integrating external cues to regulate growth and development. The most essential process of growth and development in plants is light perception and signaling. When plants are grown in dark conditions, they go through skotomorphogenesis, characterized by a pale phenotype and elongated hypocotyl. Once plants are able to perceive light, they transition to photomorphogenesis, facilitating photosynthesis and leaf development and plastid biogenesis. 

The role of single gene repositioning seems to correlate with transcriptional regulation in response to environmental factors. We implement a technique called padlock FISH which uses a rolling-circle amplification of gene-specific probes on light signaling genes, CHLOROPHYLL A/B-BINDING PROTEIN (CABs). CABs are light-inducible nuclear-encoded proteins that are important for chloroplast photosynthesis. The results of the experiments showed that in transition from dark to light conditions, the CAB genes were observed to move from the center of the nucleus to the periphery. In photoreceptor mutants, CAB repositioning was affected along with its gene activation using qRT-PCR of known light induced genes. 

Our research provides a novel perspective on light perception and regulation in plants and our findings could be harnessed to induce gene expression through spatial positioning to improve crop yield in various light conditions. The implications of this study may elucidate a gene positioning and regulation that is applicable to all eukaryote systems. 

This abstract is based on a previously published paper Feng. et al 2014, Nat. Commun from the Chen lab which can be found here: