Genome responses to environmental signals in photosynthetic organisms
Goal To understand the influence of the environment on genomes of plants and marine diatoms.
The ability to respond appropriately to a variable environment is essential for the survival of photosynthetic organisms in both terrestrial and aquatic environments. The mechanisms by which the environment can influence genome structure and dynamics are also likely to be important in driving evolution. In order to investigate these processes we use Arabidopsis thaliana as a higher plant model, and the diatom Phaeodactylum tricornutum as a model marine phytoplankton. In Arabidopsis we are examining the influence of light on chromatin-level regulation. We are exploring the changes in genome structure mediated by morphogenic light signals during the dark to light transition in young seedlings, as well as the influence of phototoxic signals such as ultraviolet wavelengths. In parallel we are using Phaeodactylum to explore the role of epigenetic phenomena in regulating phytoplankton life histories, in particular during the rise and fall of seasonal blooms.
Major advances in diatom biology are represented by the development of methodologies for gene manipulation, including RNAi, as well as the complete sequencing of diatom genomes. We are now using these resources to explore the role of epigenetic phenomena in Phaeodactylum. Most recently, we have generated epi-genome maps of this diatom that include DNA methylation data as well as selected histone mark distributions. Over recent years, we have also used genome-enabled approaches to better understand diatom responses to other environmental signals, such as light and nutrients. We are now testing the relevance of these findings in natural environments as part of the Tara Oceans expedition, a three-year circumnavigation of the world’s oceans to explore the functional biodiversity of marine microscopic life.
Our work on Arabidopsis is aimed at determining the role of chromatin-based mechanisms associated with light perception. As a model system, we use the photomorphogenic developmental switch that plant seedlings undergo when they reach the soil surface (known as de-etiolation). We found that DET1, a major repressor of photomorphogenesis, is able to bind histones. We now use this factor as a tool to assess the role of chromatin modifications in the regulation of light-responsive genes. Our recent results reveal a connection between DET1 and monoubiquitinated histone H2B marks throughout the Arabidopsis genome. They also point towards a role for DET1 in nucleotide excision repair in response to UV light. To extend this knowledge, we aim to investigate the spatial and temporal chromatin dynamics associated with light-driven transcriptional changes using a combination of genomic, molecular and cytogenetics approaches.
Selected recent publications
• Huysman MJ, Fortunato AE, Matthijs M, Costa BS, Vanderhaeghen R, Van den Daele H, Sachse M, Inzé D, Bowler C, Kroth PG, Wilhelm C, Falciatore A, Vyverman W, De Veylder L. AUREOCHROME1a-Mediated Induction of the Diatom-Specific Cyclin dsCYC2 Controls the Onset of Cell Division in Diatoms (Phaeodactylum tricornutum). Plant Cell. (2013).
• Bourbousse C.*, Ahmed I.*, Roudier F., Zabulon G., Blondet E., Balzergue S., Colot V., Bowler C., Barneche F. Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis. PLoS Genet.. (2012) 8(7):e1002825.
•Allen AE, Moustafa A, Montsant A, Eckert A, Kroth PG, Bowler C. Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms. Mol Biol Evol.. (2012) 1: 367-379.