Date : 28/04/2010
Internship proposal for : Master 1
CNRS UPS3201 Genopole, CNRS, University of Evry
Genopole Campus 1 - Genavenir 6 5 rue Henri Desbruères 91000 Evry
Director : François KEPES
Website : http://www.epigenomique.genopole.fr/~kepes/
Main discipline : Molecular biologySystems Biology
phone : +33 169474431
Subjects / Tools-Methodologies
1 : Integrative Biology/systems and synthetic biology
2 : Chromosome structure and evolution/cell biology
3 : Functional organization of cell nucleus-nucleoid/bioinformatics
Summary of lab's interests
GIP Genopole® hosts an Institute of Complex Studies dedicated to modelling and simulation of complex biological processes in the post-genomic era, called the Epigenomics Project, and headed by F. Képès. The Epigenomics Project is a CNRS Unit and is the object of contracts between GIP Genopole® and University of Evry. This lab includes computer scientists, physicists and biologists / bioinformaticists. It has a long-standing tradition of multidisciplinary projects. At the Epigenomics Project, the MEGA team has pioneered the analysis of eukaryotic networks of transcriptional interactions in 2002, and the unfolding of such networks in the cellular space since 2003.
Summary of project
The main goal of this project is to provide the quantitative fine-grained relation between gene expression level and gene position along the chromosome. This relation is studied as such, independently of any assumption, as well as in a solenoidal coordinate system suggested by previous and ongoing studies demonstrating regularities in microbial co-regulated genes positioning. To shed light on this function that governs transcription optimization in relation to genomic position, observations with original bioinformatics and signal processing tools developed in the lab will be applied to transcriptomic and genomic data, yielding a density function. This study will be extended from bacterial genomes to eukaryotic ones, starting with the nematode C. elegans and, time permitting, moving on to mammals. At stakes are an integrated spatio-temporal understanding of the functional organization of the nucleus/nucleoid, an assessment of the impact of transcriptional dynamics in shaping genome architecture along the evolution, and our capacity to rationally engineer whole microbial genomes.