Unité de Génétique        
Moléculaire des Levures        
Institut Pasteur        
25-28, Rue du Docteur Roux        
75724 Paris Cedex 15 FRANCE        
    

   
   
 

In Silico Genome Analysis in Hemiascomycetous Yeasts:

 

Comparative genomics in fungi
Ingrid Lafontaine

Molecular evolution of genes and gene families

Network analysis

 

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An example of identified pseudogenes in the genome of Saccharomyces
cerevisiae (white rectangles)

Selected References


Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H. (2006). The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res., 34, 1816-35.


Richard GF, Kerrest A, Lafontaine I, Dujon B.(2005). Comparative genomics of hemiascomycete yeasts: genes involved in DNA replication, repair, and recombination. Mol Biol Evol,4, 1011-23.


Fabre E, Muller H, Therizols P, Lafontaine I, Dujon B, Fairhead C. (2005). Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol, 4, 856-73.


Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, et al. (65 auteurs) (2004). Genome evolution in yeasts. Nature, 430, 35-44.


Lafontaine I, Fischer G, Talla E, Dujon B. (2004). Gene relics in the genome of the yeast Saccharomyces cerevisiae. Gene, 335,1-17.

 

 

Intercompartment DNA transfer
Odile Kalogeropoulos, Christine Sacerdot

In silico systematic inventory and analysis of fragments of mitochondrial and plasmid DNA found in nuclear genomes of this phyllum

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In silico genome comparisons; Genomes and genes evolution
Fredj Tekaia

Evolution of gene and protein families

Protein families evolution by motifs

Genome Data Exploration using Correspondence Analysis :

  • Fundamental signatures and global trends in amino acid composition of proteomes
  • "Genome tree" construction based on conservation profiles, orthologs and conservation weights as deduced from large scale proteome comparisons

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Selected References: http://www.pasteur.fr/~tekaia/tekaia.publications.html

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Structure and maintenance of chromosomes/Mating type
Cécile Fairhead, Héloïse Muller

 

Structure and maintenance of chromosomes:

subtelomeric regions: duplications and recombinations

telomeres and telomerases

double-strand break repair

Mating type:

plasticity of sexual reproduction in fungi, "MAT" regions

 

Selected References


Muller H., Hennequin C., Dujon B., Fairhead C. 2007. Comparing MAT in the genomes of hemiascomycetous yeasts. In "Sex in fungi:  molecular determination and evolutionary implications", (Eds: J. Heitman, J. Kronstad, J. Taylor, and L. Casselton), ASM Press


Muller H., Dujon B., Fairhead C. 2007. Comparative genomics in hemiascomycetous yeasts. In "Candida: comparative and functional genomics", (Eds: C. Denfert and B. Hube), pp 71-92, Caister Academic Press.


Fairhead C., Dujon B. 2006. Structure of K. lactis subtelomeres: duplications and gene content. FEMS Yeast Research, 6(3):428-41.


Therizols P., Fairhead C., Cabal GG., Genovesio A., Olivo-Marin JC., Dujon B., Fabre E. 2006. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J Cell Biol. 172(2):189-99.


Fabre E., Muller H., Therizols P., Lafontaine I., Dujon B., and Fairhead C. 2005. Comparative genomics in hemiascomycetous yeasts: evolution of sex, silencing and subtelomeres. Mol Biol Evol 22(4):856-73.


Ricchetti M., Dujon B., Fairhead C. 2003. Distance from the chromosome end determines the efficiency of DSB repair in subtelomeres of haploid yeast. J Mol Biol. 328: 847-62.


Ricchetti M., Fairhead C., Dujon B. 1999. Mitochondrial DNA repairs double strand breaks in yeast chromosomes. Nature 402: 96-100.

   
 

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Nuclear Architecture
Emmanuelle Fabre, Pierre Therizols

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Our questions are focused on functional organization of yeast nuclei  (Saccharomyces cerevisiae and other hemiascomycetes). We are interested in how nuclear and chromosomal context play a role on genome stability and gene expression. By using live imaging techniques we have analysed the localization of one particular chromosome end and characterized its peripheral positioning. We could correlate this subnuclear localization to double strand repair efficiency in subtelomeres. We are characterizing how the nuclear context could affect genome stability in particular chromosomal compartments and defining localization of chromosomal ends by high throughput analyses. We aim at defining the conservation of chromosomal organization.

Double labelling of two different chromosome ends visualised by insertion of TetO and lacO arrays

Our main objectives are:

  1. To understand the role of Nuclear Pore complexes on chromatin localization and DSB repair
  2. To understand the spatial organization of chromosome ends within the nucleus and its functional implications on genome stability
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One major component of the nuclear architecture corresponds to the Nuclear Pore Complexes (NPCs).
Yeast NPCs are formed by 30 individual nucleoporins that can assemble in particular subcomplexes (i.e Nup84 complex).
We have found that preferential localization of chromosome ends at the nuclear periphery is lost in Nup84 complex mutants.
Chromatin silencing found at the end of most chromosome ends is also lost in Nup84 complex mutants.
Double strand break repair occurring in subtelomeres is severely impaired in these mutants

Yeast Saccharomyces cerevisiae nucleus seen by electron microscopy.
NPCs embedded in the double nuclear envelope are visible

Selected References


THERIZOLS, P., C. FAIRHEAD, G. G. CABAL, A. GENOVESIO, J. C. OLIVO-MARIN, , B. DUJON and E. FABRE, 2006 Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J Cell Biol 172: 189-199.


FABRE, E., 2006 [Nuclear pore and functional organization of chromatin]. Med Sci (Paris) 22: 483-484.


FABRE, E., H. MULLER, P. THERIZOLS, I. LAFONTAINE, B. DUJON et al., 2005 Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 22: 856-873.


DUJON, B., D. SHERMAN, G. FISCHER, P. DURRENS, S. CASAREGOLA et al., 2004 Genome evolution in yeasts. Nature 430: 35-44.


TEIXEIRA, M. T., B. DUJON and E. FABRE, 2002 Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae. J Mol Biol 321: 551-561.


TEIXEIRA, M. T., E. FABRE and B. DUJON, 1999 Self-catalyzed cleavage of the yeast nucleoporin Nup145p precursor. J Biol Chem 274: 32439-32444.


TEIXEIRA, M. T., S. SINIOSSOGLOU, S. PODTELEJNIKOV, J. C. BENICHOU, M. MANN et al., 1997 Two functionally distinct domains generated by in vivo cleavage of Nup145p: a novel biogenesis pathway for nucleoporins. Embo J 16: 5086-5097.


FABRE, E., and E. HURT, 1997 Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31: 277-313.


FABRE, E., N. L. SCHLAICH and E. C. HURT, 1995 Nucleocytoplasmic trafficking: what role for repeated motifs in nucleoporins? Cold Spring Harb Symp Quant Biol 60: 677-685.


FABRE, E., and E. C. HURT, 1994 Nuclear transport. Curr Opin Cell Biol 6: 335-342.


FABRE, E., W. C. BOELENS, C. WIMMER, I. W. MATTAJ and E. C. HURT, 1994 Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif. Cell 78: 275-289
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Mini and Microsatellite instabilities
Guy-Franck Richard, Alix Kerrest

 

We are interested in understanding how DNA tandem repeats, like microsatellites and minisatellites are born, evolve and disappear. Trinucleotide repeats, a particular class of microsatellites, are involved in a growing number of human neurological disorders, including X-fragile, Huntington disease and several types of ataxias. The pathology is always associated to the large expansion of a trinucleotide repeat within or near a gene. We have shown that these expansions, in yeast, occur both during DNA replication and homologous recombination. We have isolated two genes, SGS1 and SRS2 (encoding DNA helicases conserved from bacteria to humans) that are involved in stabilizing trinucleotide repeats. We now try to understand the tight links between replication and homologous recombination and how these two metabolic pathways interact with each other.

Minisatellites are longer tandem repeats, also found in all eukaryotic genomes. By comparative genomics, we have shown that they evolve faster than the genes containing them. The mechanisms underlying birth, fast evolution and death of minisatellites are currently under investigation.

Our main questions are:

  1. How do DNA helicases interplay in stabilizing tandem repeats in vivo?
  2. How do replication and homologous recombination interact with each other during the cell cycle?
  3. What are the molecular mechanisms involved in the de novo formation of tandem repeats?

In order to adress these questions, we use classical reverse genetics and molecular biology approaches, such as conditional mutants, DNA two-dimensional gel electrophoreses and chromatin immunoprecipitation.

 

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 A model showing three different pathways to repair replication fork-damage due to trinucleotide repeat-dependent structures. Top: Srs2 and Sgs1 helicases act at the fork to facilitate replication across structure-forming sequences. In the absence of either of these helicases, single-strand gaps or double-strand breaks result Left arrow: Srs2p can also facilitate fork regression, perhaps by removing Rad51 from damaged forks, to allow bypass of the damage and fork restart in a manner that prevents breakage and repeat length changes. Middle downward arrows: Single-strand or double-strand breaks can be processed by a Rad51-dependent sister chromatid recombination pathway, leading to recombination intermediates that are dissolved by Sgs1p-Top3p. Hairpin formation by CAG/CTG repeats during strand invasion can lead to repeat contractions or expansions depending on the location of the hairpin. Joint molecules observed by 2D gels (shown inside the grey box) correspond to either regressed forks or Rad51-dependent sister chromatid recombination intermediates.

Selected References


G.-F. Richard, B. Dujon AND J. E. Haber (1999). Double-strand break repair can lead to high frequencies of deletions within short CAG/CTG trinucleotide repeats. Mol. Gen. Genet. 261: 871-882


G.-F. Richard, C. Hennequin, A. Thierry and B. Dujon (1999). Trinucleotide repeats and other microsatellites in yeasts. Res. Microbiol. 150: 589-602


G.-F. Richard, G. M. Goellner, C. T. McMurray and J. E. Haber (2000). Recombination-induced CAG trinucleotide repeat expansions in yeast involve the MRE11 /RAD50/XRS2  complex EMBO J. 19 : 2381-2390


G.-F. Richard and F. Pâques (2000). Mini- and microsatellite expansions : the recombination connection. EMBO Reports : 122-126


F. Pâques, G.-F. Richard and J. E. Haber (2001). Expansions and contractions in 36-bp minisatellites by gene conversion in yeast. Genetics 158: 155-166


G.-F. Richard, C. Cyncynatus and B. Dujon (2003). Contractions and expansions of CAG/CTG trinucleotide repeats occur during ectopic gene conversion in yeast, by a MUS81-independent mechanism. J. Mol. Biol. 326: 769-782


A. Malpertuy, B. Dujon and G.-F. Richard (2003). Analysis of microsatellites in 13 hemiascomycetous yeast species: mechanisms involved in genome dynamics. J. Mol. Evol. 56: 730-741


S. Loeillet, B. Palacande, M. Cartron, A. Thierry, G.-F. Richard, B. Dujon, V. Doye and A. Nicolas (2005) Genetic network interactions among replication, repair and nuclear pore deficiencies in yeast. DNA Repair 4: 459-468


G.-F. Richard and B. Dujon (2006) Molecular evolution of minisatellites in hemiascomycetous yeasts. Mol Biol Evol. 23:189-202


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Chromosomal Rearrangements and Genome Evolution
Gilles Fischer, Celia Payen

 

Despite the numerous pathways that aim at preserving genome integrity (DNA recombination and repair, cell cycle checkpoints, etc…), chromosomes are very dynamic structures that accumulate rearrangements over time. These rearrangements (duplications/deletions, translocations, inversions) lead to the modification of both the gene order and the gene content of the genomes and therefore have profound effect onto the evolution of species. We are interested in understanding the phenomenology, the molecular mechanisms as well as the selective impact of chromosomal rearrangements onto genome evolution. We developed a complementary approach between experimental genetics in Saccharomyces cerevisiae and in silico analyses of genomic data from different Hemiascomycetous yeast species.

Our main questions are:

  1. How gene order is reorganized between genomes of related species?
  2. How segmental duplications are generated in a genome?
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Schematic representaion of gene order re-assortment between chromosome D of S. cerevisiae (Sc_D) and the 13 chromosomes of C. glabrata (Cg_A to Cg_M)

 

Selected References


KOSZUL, R., B. DUJON and G. FISCHER, 2006 Stability of large segmental duplications in the yeast genome. Genetics 172: 2211-2222.


FISCHER, G., E. P. ROCHA, F. BRUNET, M. VERGASSOLA and B. DUJON, 2006 Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLoS Genet 2: e32.


KOSZUL, R., S. CABURET, B. DUJON and G. FISCHER, 2004 Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. Embo J 23: 234-243.


DUJON, B., D. SHERMAN, G. FISCHER, P. DURRENS, S. CASAREGOLA et al., 2004 Genome evolution in yeasts. Nature 430: 35-44.


FISCHER G., NEUVEGLISE C., DURRENS P., GAILLARDIN C. AND B. DUJON. Evolution of gene order in the genomes of two related yeast species. (2001) Genome Research, .11, 2009-2019.


FISCHER G., JAMES S.A., ROBERTS I.N., OLIVER S.G. AND E.J. LOUIS. Chromosomal evolution in Saccharomyces. (2000) Nature, 405, 451-454

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