Section: Overall Objectives

Highlights

There are two highlights we wish to stress for 2011. One is scientific and relates to contributions we made this year to the problems of intra- and inter-chromosomal interactions. The other highlight is both scientific and organisational. It concerns the setting up of an INRIA International Partnership with our close collaborators in Italy and the Netherlands.

Intra- and inter-chromosomal interactions

This year, we were able to make two contributions which both rely on the use of recently published data of 3D co-localisation of DNA fragments in human cells. In both cases, our findings are novel and broaden our view of what is a gene and what drives its (change of) location on the genome.

On the one hand, from the joint study of the network of spatial proximities of human genomic loci and a dataset of evolutionary breakpoints between human and mouse, we were able to provide evidence that evolutionary breakpoints tend to cluster spatially in human cells, which leads us to propose the new notion of spatial synteny, which generalises the widely used concept of genomic synteny.

On the other hand, in the framework of the extension of the ENCODE project to chromosome 21 and 22, we had the opportunity to identify a new category of transcripts, which we call chimeric transcripts. These transcripts contain exons from different genes, which can themselves be located far apart on the same chromosome, or on different chromosomes. We further found that the network formed by these connected genes is enriched in cliques of sizes 3 and 4, which seems to indicate that transcription and/or splicing of these sets of genes co-occur in time and space, as is confirmed by the confrontation of our expression dataset to a dataset indicating the co-localisation of DNA fragments in 3D.

INRIA International Partner: AMICI

The INRIA International Partner project AMICI is the continuation and extension of the INRIA Associated Team SIMBIOSI that started in January 2009 and ended in December 2011 (see the web page for SIMBIOSI at http://pbil.univ-lyon1.fr/members/sagot/htdocs/team/projects/simbiosi/simbiosi.html ). It includes, beside the EPI, four partners: University of Rome La Sapienza, group headed by Alberto Marchetti-Spaccamela; Free University of Amsterdam and CWI, group headed by Leen Stougie; University of Florence, group headed by Pierluigi Crescenzi; University of Pisa, group headed by Nadia Pisanti. More information on AMICI may be found at http://piluc.dsi.unifi.it/amici .