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Accueil > Départements > Biologie des Génomes > Linda SPERLING : Analyse du Génome

Linda SPERLING : Présentation de l’équipe

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Our team is interested in the organisation, evolution and stability of genomes. Our research seeks to understand how DNA metabolism (replication, recombination, repair, transposition) and the regulation of transcription (gene expression, chromatin structure, non-coding RNAs) act over time on the sequence, organization and dynamics of genomes.

Paramecium genome

— Annotation of the somatic and germline genomes of the P aurelia complex of 15 sibling species
— Programmed genome rearrangements : mechanisms of recognition of the germline elements that are excised from the genome during somatic differenciation
— Development of the community model organism database ParameciumDB

Major achievements in recent years
-  Demonstration that the Paramecium genome was shaped by a series of whole genome duplications (Nature 2006, Genome Research 2008).
-  Translational control of eukaryotic intron splicing (Nature 2008).
-  Origin and evolution of 45,000 germline-limited "Internal Eliminated Sequences" in Paramecium (PLoS Genetics 2012).
-  Exaptation of genome defense sRNAs for epigenetic mating type inheritance (Nature 2014).

Collaborations
-  Mireille Bétermier (I2BC, Gif) functional genomics
-  Sandra Duharcourt (IJM, Paris) functional genomics
-  Eric Meyer (IBENS, Paris) functional genomics, annotation
-  Laurent Duret, (LBBE, Villeurbanne) biostatistics, evolutionary biology
-  Mariusz Nowacki (University of Bern, Switzerland) functional genomics
-  Jacek K. Nowak (IBB, Warsaw, Poland) functional genomics

Animal genomes

— spatio-temporal vetebrate replication program
— impact of replication on the evolution, organisation and stability of genomes
— chromatin structure and dynamics
— Scientific direction of the ImaGif high throughput sequencing platform.

Major achievements in recent years
1. Discovery of a new class of regulatory ncRNA (XUT) genes in Saccharomyces cerevisiae (Van Dijk Nature 2011) ;
2. Determination of one of the first high resolution replication timing profiles of the human genome (Chen Genome Res. 2010) ;
3. Discovery of the mammalian mutation rates increase during the late replicating S phase (Chen Genome Res. 2010) ;
4. Demonstration for the first time of the existence of mutational asymmetries associated with replication in eukaryotes (Chen Mol. Bio. Evol. 2011) ;
5. Evidence of megabase replication domains related to higher-order chromatin structure (Guilbaud PLOS Comp. Biol. 2011, Baker PLOS Comp. Biol. 2012 ; Audit Nature Protoc. 2013) ;
6. Generation of the first high-resolution replication fork directionality profiles of human cells by deep sequencing of purified Okazaki fragments (manuscript in preparation) ;
7. Coupling between nucleosome phasing and splicing efficiency in Paramecium (manuscript in preparation).

Collaborations
Biologists :
O. Hyrien (ENS, Paris) : human replication program
M. Debatisse (Curie, Paris) : common fragile site activity
M. Bétermier (CGM, Gif-sur-yvette) and S. Duhacourt (IJM, Paris) : Paramecium biology
A. Morillon (Curie, Paris) : yeast ncRNA
A. Taddei (Curie, Paris) : compartmentalization and dynamics of nuclear functions
Physicists :
A. Arneodo and B. Audit (ENS, Lyon) : multi-scale analysis
C. Vaillant (ENS, Lyon) : physical modeling of nucleosome positioning

Keywords

genomics and epigenomics, evolution, replication, genome rearrangements, non-coding RNA, transposable elements, annotation, NGS, Paramecium, human

Contact


SPERLING Linda [Directeur de Recherche Emérite - CNRS]
Equipe Betermier M. - Réarrangements programmés du génome
01 69 82 32 09 Gif - Bât 26

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