Plant and diatom genomics
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. 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.
Epigenomics. 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, including nitrogen and iron.
The Tara Oceans expedition. We are now testing the relevance of these findings in natural environments as part of the Tara Oceans expedition, a four-year circumnavigation of the world’s oceans to explore the functional biodiversity of marine microscopic life.
To know more about Diatom research
Our work on Arabidopsis is aimed to determine the role of chromatin-based mechanisms in plant adaptive responses to environmental cues, with a specific emphasis on light conditions.
In this research line, the team investigates the impact of chromatin organization and composition dynamics on the regulation of gene expression. This is achieved by integrating spatial and temporal chromatin variations with transcriptional changes in response to light perception. This study enabled us to identify light-regulated genes whose upregulation following light perception is optimized by rapid changes of local chromatin states. This gene list comprises several master regulators of plant light responses and circadian clock function. The team also explores how nucleus higher-order organisation is controled by light signaling components, and reciprocally, the potential contribution of the spatial chromatin organisation on transcriptional reprogramming in response to light cues.
To know more about Arabidopsis research
• Bailleul, B., Berne, N., Murik, O., Petroutsos, D., Prihoda, J, Tanaka, A., Villanova, V., Bligny, R., Flori, S., Falconet, D., Krieger-Liszkay, A., Santabarbara, S., Rappaport, F., Joliot, P., Tirichine, L., Falkowski, P. G., Cardol, P., Bowler, C. and Finazzi, G. (2015) Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms. Nature. 524: 366-369.
• Bourbousse C, Mestiri I, Zabulon G, Bourge M, Formiggini F, Koini MA, Brown SC, Fransz P, Bowler C, Barneche F. (2015) Light signaling controls nuclear architecture reorganization during seedling establishment. Proc Natl Acad Sci U S A. May 11.
• Veluchamy A, Rastogi A, Lin X, Lombard B, Murik O, Thomas Y, Dingli F, Rivarola M1, Ott S, Liu X, Sun Y, Rabinowicz PD, McCarthy J, Allen AE1, Loew D, Bowler C, Tirichine L. (2015) An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biol.. May 20;16(1):102.
• Morrissey J, Sutak R, Paz-Yepes J, Tanaka A, Moustafa A, Veluchamy A, Thomas Y, Botebol H, Bouget FY, McQuaid JB, Tirichine L, Allen AE, Lesuisse E, Bowler C. A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake. Curr. Biol.. (2015) 25: 364-71.
• Veluchamy, A., Lin, X., Maumus, F., Rivarola, M., Bhavsar, J., Creasy, T., O’Brien, K., Sengamalay, N. A., Tallon, L. J., Smith, A. D., Rayko, E., Ahmed, I., Le Crom, S., Farrant, G. K., Sgro, J.-Y., Olson, S. A., Splinter Bondurant, S., Allen, A., Rabinowicz, P. D., Sussman, M. R., Bowler, C. and Tirichine, L. Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nature Comm.. (2013) 4: 2091
• Bourbousse C.*, Ahmed I.*, Roudier F., Zabulon G., Blondet E., Balzergue S., Colot V., Bowler C., Barneche F. (2012) Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis. PLoS Genet.. 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.
• Castells E., Molinier J., Benvenuto G., Bourbousse C., Zabulon G., Zalc A., Cazzaniga S., Genschik P., Barneche F., and C. Bowler. (2011) The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress. EMBO J. 30: 1162-72.
• Fernie AR, Obata T, Allen AE, Araújo WL, Bowler C. Leveraging metabolomics for functional investigations in sequenced marine diatoms. Trends Plant Sci.. (2012) 17: 395-403.
• Allen AE, Dupont CL, Oborník M, Horák A, Nunes-Nesi A, McCrow JP, Zheng H, Johnson DA, Hu H, Fernie AR, Bowler C. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature. (2011) 473: 203-207.