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Habilitation à diriger des recherches

La fluidité des génomes

Eric Coissac 1
1 HELIX - Computer science and genomics
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Since the publication of the two first fully sequenced genomes (Haemophilus influenzae and Saccharomyces cerevisiae) in the second half of nineties, biology has entered a new phase. After the era of molecular biology, at times described as reductionist biology, the new genomic era has incited biologists to adopt a more integrative point of view. This new emphasis on what has been called "integrative biology", has fled to the awareness that the simplistic idea according to which the knowledge of the full list of genes of an organism is enough to understand its functioning is not realistic, even if it has justified many genome projects.

I was lucky to begin my research work at the same time the genome projects started. I participated in the yeast genome project leading to the full sequence of the first eukaryotic genome in 1997. I do not know if it is by opposition to the simplistic idea described above, but since that time I have been working on chromosome evolution as independently as possible of the genes they support. I have tried through my work to highlight evolutionary constraints associated to DNA structure and not to its information contents.

For this reason, I am mainly studying duplication mechanisms which explain many of the chromosomal rearrangements. A model issued from this work has been proposed. It explains the origin and fate of observable duplications in genomes. It seems to be applicable, to a large extend, to the three super-kingdoms (Eukaryota, Eubacteria and Archea), which is for me a good indication of the ancestral aspects of the underlying mechanism.

Even if this approach independently of gene function has its interest, it would undoubtedly not be reasonable to continue this type of work without trying to connect the results obtained so far with data on the information carried by the chromosomes and thus with the function of genes encoded by them. Establishing a link between data on repeats available to me and functional data available in public database is a challenge which involves data integration and knowledge representation. MicrOBI can be regarded as my response to this problem. Today, this database allows the maintenance of coherent existing links between several public databases describing different type of biological information. Adding data on chromosomal repeats to the present schema will allow the construction of complex requests integrating different levels of information such as genome, proteome and functional classification.
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Habilitation à diriger des recherches
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Eric Coissac. La fluidité des génomes. Autre [q-bio.OT]. Université Pierre et Marie Curie - Paris VI, 2005. ⟨tel-00011102⟩

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