Chromatin remodelling in light signalling

Plants selectively deplete incident light of red (R) wavelength, relative to far-red (FR) wavelength light. Consequently, the relative proportions of R and FR (R:FR ratio) act as an indicator of surrounding vegetation and plants, via the phytochrome photoreceptors, are capable of detecting this. Low R:FR ratio is interpreted as surrounding competition and results in plants eliciting, what is known as, the shade avoidance response. This involves a host of both phenotypic and molecular changes, including increased hypocotyl growth, earlier flowering time and changes in gene expression. The fundamental mechanisms underlying R:FR-mediated changes in gene expression are not fully characterised. Given that increasing evidence in Arabidopsis suggests that the structure of chromatin is integral in the regulation of gene expression in response to environmental stimuli, it was investigated to see if this was the case in R:FR ratio signalling. Here, DNaseI sensitivity assays demonstrate that the shade avoidance genes ATHB2, PIL1 and XTH15 all undergo gross changes in chromatin structure in plants grown in light/dark cycles and treated with low R:FR ratio. These low R:FR induced changes in DNaseI sensitivity are conspicuously absent when plants are grown in continuous light, suggesting an involvement of the circadian clock. Complementary to this, the use of ChIP has identified the coding region of PIL1 to show increased association with hyper-acetylated H3K9 and possibly H3K14 in response to low R:FR ratio. Together, this work demonstrates that changes in R:FR ratio induce changes in gene expression that are correlated with changes in chromatin structure and histone modifications and that these changes could be regulated by the circadian clock. In addition, the identification and construction of multiple mutant and transgenic lines expressing altered levels of chromatin modifying protein was attempted.