Our lab

Delphine Naquin, Engineer NGS deep sequencing platform

Yves d'Aubenton-Carafa, Engineer, CNRS

Chunlong Chen, Researcher CNRS

Yan Jaczszyszyn, Engineer

Maud Silvain, Engineer, CNRS

Claude Thermes, Researcher, CNRS

Erwin Van Dijk, Engineer NGS deep sequencing platform

Address

CNRS - Centre de Génétique Moléculaire

Avenue de la Terrasse - Bât. 24

91198 GIF-SUR-YVETTE Cedex

France

Phone : 33 (0)1 69 82 38 28

Telecopy : 33 (0)1 69 82 38 77

Current Research

Genome evolution leads to the presence in genome sequences of different types of information, like the coding and maintenance of the genetic information, the vestiges of evolutionary events, but also the signatures of various essential cellular processes like replication or DNA compaction in chromatin. We study how is encoded, in genome sequences, the information related to mechanisms like replication, transcription, or those involved in chromosome organization and dynamics. We study the mutational biases associated to transcription and to replication and how they allow the identification of replication origins in vertebrate genomes (http://replicor.cgm.cnrs-gif.fr/index.html).

Another of our research interests focuses on in silico detection and study of non protein coding RNAs, a new class of genes involved in a large number of gene regulation processes like RNA interference, imprinting or chromatin architecture. In the context of a European project we determine new non-coding RNAs in human, mouse and A thaliana (http://www.isv.cnrs-gif.fr/mc/riboreg/index.php). In the context of a project on vertebrate evolution we annotate the transcriptomes of Scyliorhinus canicula and of Lampetra fluviatilis ( http://www.cgm.cnrs-gif.fr/thermes/lamproie/projet_roussette2.html).

Selected publications

- Guilbaud, G., Rappailles, A., Baker, A., Chen, CL., Arneodo, A., Goldar, A., d'Aubenton-Carafa, Y., Thermes, C., Audit, B., Hyrien, O. (2011) Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome.
PLoS Comput Biol, 7(12):e1002322.

- Arneodo, A., Vaillant, C., Audit, B., Argoul, F., d'Aubenton-Carafa, Y., Thermes, C. (2011) Multi-scale coding of genomic information: From DNA sequence to genome structure and function.
Physics Reports-Review Section of Physics Letters, 498 (2-3) 45-188.

- Dubarry, M., Loïodice, I., Chen, C. L., Thermes, C. and Taddei, A. (2011) Tight protein-DNA interactions favor gene silencing.
Genes Dev, 25 (13) 1365-70.

- Van Dijk, E.L., Chen, C.L. , d'Aubenton-Carafa, Y., Gourvennec, S., Kwapisz, M., Roche, V., Bertrand, C., Silvain, M., Legoix-Né, P., Leoillet, S., Nicolas, A., Thermes, C. and Morrillon, A. (2011) XUT, a novel class of antisense regulatory ncRNA in yeast.
Nature, 475 (7354) 114-7.

- Chen, CL., Duquenne, L., Audit, B., Guilbaud, G., Rappailles, A., Baker, A., Huvet, M., d'Aubenton-Carafa, Y., Hyrien, O., Arneodo, A., Thermes, C. (2011) Replication-associated mutational asymmetry in the human genome.
Mol Biol Evol, 28 (8) 2327-37.

- Chen, C.-L., Rappailles, A., Duquenne, L., Huvet, M., Guilbaud, G., Farinelli, L., Audit, B., d'Aubenton-Carafa, Y., Arneodo, A., Hyrien, O. and Thermes, C. (2010) Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes.
Genome Res, 20 (4) 447-57.

- Vaillant, C., Palmeira, L., Chevereau, G., Audit, B., d'Aubenton-Carafa, Y., Thermes, C. and Arneodo, A. (2010) A novel strategy of transcription regulation by intra-genic nucleosome ordering.
Genome Res, 20 (1) 59-67.

- Chevereau, G., Palmeira, L., Thermes, C., Arneodo, A. and Vaillant, C. (2009) Thermodynamics of nucleosome ordering by genomic confinement.
Phys Rev Letters, 103 (18) 188103.

- Audit, B., Zaghloul, L., Vaillant, C., Chevereau, G., d'Aubenton-Carafa, Y., Thermes, C. and Arneodo, A. (2009) Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.
Nucleic Acids Res, 37 (18) 6064-75.

- Neil, H. , Malabat, C., d’Aubenton-Carafa, Y., Xu, Z. Steinmetz, L.M. and Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast.
Nature, 457 (7232) 1038-42.

- Ben Amor, B., Wirth, S., Merchan, F., Laporte, P., d'Aubenton-Carafa, Y., Hirsch, J., Maizel, A., Mallory, A., Lucas, A., Deragon, J.-M., Vaucheret, H., Thermes, C. and Crespi, M. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.
Genome Res, 19 (1) 57-69.

- Miele, V., Vaillant, C., d'Aubenton-Carafa, Y., Thermes, C. and Grange, T. (2008) DNA physical properties determine nucleosome occupancy from yeast to fly.
Nucleic Acids Res, 36 (11) 3746-56.

- Audit, B., Nicolay, S., Huvet, M., Touchon, M., d'Aubenton-Carafa, Y., Thermes, C. and Arneodo, A. (2007) DNA replication timing data corroborate in silico human replication origin predictions.
Physical Review Letters, 99 (24) 248102.

- Huvet, M., Nicolay, S., Touchon, M., Audit, B., d'Aubenton-Carafa, Y., Arneodo, A. and Thermes, C. (2007) Human gene organization driven by the coordination of replication and transcription.
Genome Res, 17 (9) 1278-1285.

- Touchon, M., Nicolay, S., Audit, B., Brodie of Brodie, E.B., d'Aubenton-Carafa, Y., Arneodo, A. and Thermes, C. (2005) Replication-associated strand asymmetries in mammalian genomes: Toward detection of replication origins.
Proc. Natl. Acad. Sci. USA , 102, 9836-9841.

- Touchon M, Arneodo A, d'Aubenton-Carafa Y & Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes.
Nucleic Acids Res. 32: 4969-4978.

- Nicolay S, Argoul, F, Touchon, M, d'Aubenton-Carafa, Y, Thermes C & Arneodo A (2004) Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?
Phys. Rev. Lett. 93: 108101.

- Audit, B., Vaillant, C., Arneodo, A., d'Aubenton-Carafa, Y. and Thermes, C. (2002) Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes.
J. Mol. Biol. 316: 903-918.

To know more about our work

Current research

Team & collaborations

Publications