ABOUT US
Project leaders
Fredy Barneche
After having unveiled that chromatin architecture rapidly reorganises in seedling primary leaves when they perceive light for the first time, he identified that gene transcription globally increases during this delicate transition. This groundwork set the stage to this project with the Baroux expertise. Our objective is to elucidate how spatial dynamics of transcription and epigenome adaptations influence genome regulation and plant cell responses to light. Fredy's website Team members Clara Bourbousse (CNRS research scientist) co-leads the research group with Fredy. Her major aim is to unravel the impact of plastid activities on the landscape and spatial organization of chromatin, and how these dynamics contributes to adapt the cellular transcriptional programs to the plant metabolic status.
Mhairi Davidson (Post-doc) undertakes genomics approaches to decipher gene composition and transcriptional properties of light-dependent transcriptional clusters
Geoffrey Schivre (PhD student) investigates the functional consequences of increased transcriptional activity using a quantitative transcriptomic approach
Lorenzo Concia (Post-doc) uses Chromatin Conformation Capture (Hi-c) to characterize topological features of genome reorganization during Arabidopsis responses to light.
Clarisse Zigue (PhD student) will soon join us to investigate the impact of light signaling on epigenome dynamics, and how light-induced chromatin adaptations contribute to gene expression responsiveness
Former members Leopold Carron (Post-doc)
CollaborationsAlessandra Carbone
(Associated Partner Team Leader) Her research investigates various problems connected with the functioning and evolution of biological systems. She develops mathematical tools, coming from statistics and combinatorics, algorithmic tools and molecular physics to study basic principles of cellular functioning starting from genomic data. Alessandra's website |
Célia Baroux
My research focuses on elucidating the cytological, chromatin dynamics events associated with plant cells' reprogramming, in response to developmental or environmental cues, such as light. We deploy high-resolution microscopy imaging, cytogenetics and image analysis to identify spatial patterns of chromatin re-organisation. In combination with genetic approaches we try to elucidate the mechanisms and causality of these changes. In this project, I contribute 3D image analysis and data mining thanks to DataViz a new, interactive data visualisation interface we developped in collaboration with the S3IT. Célia's website Team membersFilippo Mirasole (PhD student). Filippo will analyse the mechanisms controlling the spatial reorganisation of transcription during the light-to-dark transition, focusing on candidate photoreceptors. In collaboration with the Barneche-Bourbousse group, he will also analyse the positioning of light-induced transcriptional clusters
Kinga Rutowicz (post doc). Kinga investigates the transcriptional changes under the diurnal light rythm that are controlled by linker histones
Lena Perseus (master student). Lena investigates the cytological changes in chromatin organisation under the diurnal light rythm
Former members
Ricardo Randall (post-doc) Ricardo developped the workflow to visualize RNA Pol II clusters by immunostaining and image them at nanoscale using STED imaging. UHe used Imaris to process the 3D images and map the transcription clusters in the nucleus space.
CollaborationsDevin Routh. Devin developped an R-Shiny based interface to interactively plot the multidimensional data we obtain from our 3D images. He implemented scripts for data cleaning, data normalisation and the creation of customised variables, together with a set of very handy functions for 1D and 2D plots. Check out DataViz functionalities in the guidelines!
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