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Guy-Franck Richard

Bio: Guy-Franck Richard is an academic researcher from Pasteur Institute. The author has contributed to research in topics: Genome & Trinucleotide repeat expansion. The author has an hindex of 27, co-authored 56 publications receiving 4416 citations. Previous affiliations of Guy-Franck Richard include Brandeis University & Pierre-and-Marie-Curie University.


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Journal ArticleDOI
01 Jul 2004-Nature
TL;DR: Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Abstract: Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.

1,604 citations

Journal ArticleDOI
TL;DR: The nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences are described and a unified definition for mini- and microsatellites is proposed that takes into account their biological properties.
Abstract: Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

489 citations

Journal ArticleDOI
Bernard Dujon1, Despina Alexandraki2, Bruno André3, W. Ansorge, Victoriano Baladrón4, Juan P. G. Ballesta5, Andrea Banrevi, P. A. Bolle, Monique Bolotin-Fukuhara6, Peter Bossier7, Germán Bou5, J. Boyer1, M. J. Buitrago4, Geneviève Chéret, Laurence Colleaux1, B. Dalgnan-Fornier6, F. del Rey4, Caroline Dion, H. Domdey, A. Düsterhöft, S. Düsterhus8, K. D. Entian8, Holger Erfle, Pedro F. Esteban4, Heidi Feldmann9, L. Fernandes7, G. M. Fobo, C. Fritz, Hiroshi Fukuhara, C. Gabel, L. Gaillon1, J. M. Carcia-Cantalejo5, José J. García-Ramírez4, Manda E. Gent10, Marjan Ghazvini11, Marjan Ghazvini1, André Goffeau12, A. Gonzaléz4, Dietmar Grothues, Paulo Guerreiro7, Johannes H. Hegemann, N. Hewitt, François Hilger, Cornelis P. Hollenberg, O. Horaitis13, O. Horaitis2, Keith J. Indge10, Alain Jacquier1, C. M. James10, J. C. Jauniaux14, J. C. Jauniaux3, A. Jimenez5, H. Keuchel, L. Kirchrath, K. Kleine, Peter Kötter8, Pierre Legrain1, S. Liebl, Edward J. Louis15, A. Maia e Silva7, Christian Marck, A.-L. Monnier1, D. Mostl, Sylke Müller, B. Obermaier, Stephen G. Oliver10, C. Pallier6, Steve Pascolo1, Steve Pascolo11, Friedhelm Pfeiffer, Peter Philippsen, Rudi J. Planta16, Fritz M. Pohl17, Thomas Pohl, Regina Pohlmann, Daniel Portetelle, Bénédicte Purnelle12, V. Puzos6, M. Ramezani Rad, S. W. Rasmussen18, Miguel Remacha5, José L. Revuelta4, Guy-Franck Richard1, Martin Rieger, Claudina Rodrigues-Pousada7, Matthias Rose8, Thomas Rupp, Maria A. Santos4, Christian Schwager, Christoph Wilhelm Sensen, J. Skala12, J. Skala19, Helena Soares7, Frédéric Sor, J. Stegemann, Hervé Tettelin12, Alain R. Thierry1, M. Tzermia2, L. A. Urrestarazu3, L Van Dyck12, J. C. van Vliet-Reedijk16, Michèle Valens6, M. Vandenbo, C. Vilela7, Stephan Vissers3, D. von Wettstein18, H. Voss, Stefan Wiemann, G. Xu, Jürgen Zimmermann, M. Haasemann6, I. Becker, Hans-Werner Mewes 
02 Jun 1994-Nature
TL;DR: The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined, and the 666,448-base-pair sequence has revealed general chromosome patterns.
Abstract: The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.

383 citations

Journal ArticleDOI
TL;DR: Five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that are called "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication, are concentrated here on.
Abstract: Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.

221 citations

Journal ArticleDOI
TL;DR: This work shows the possibility to readily identify S. boulardii (a strain increasingly isolated from invasive infections) using a unique and specific microsatellite allele.
Abstract: Since Saccharomyces cerevisiae appears to be an emerging pathogen, there is a need for a valuable molecular marker able to distinguish among strains. In this work, we investigated the potential value of microsatellite length polymorphism with a panel of 91 isolates, including 41 clinical isolates, 14 laboratory strains, and 28 strains with industrial relevance. Testing seven polymorphic regions (five trinucleotide repeats and two dinucleotide repeats) in a subgroup of 58 unrelated strains identified a total of 69 alleles (6 to 13 per locus) giving 52 different patterns with a discriminatory power of 99.03%. We found a cluster of clinical isolates sharing their genotype with a bakery strain, suggesting a digestive colonization following ingestion of this strain with diet. With the exception of this cluster of isolates and isolates collected from the same patient or from patients treated with Saccharomyces boulardii, all clinical isolates gave different and unique patterns. The genotypes are stable, and the method is reproducible. The possibility to make the method portable is of great interest for further studies using this technique. This work shows the possibility to readily identify S. boulardii (a strain increasingly isolated from invasive infections) using a unique and specific microsatellite allele.

211 citations


Cited by
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3,734 citations

Journal ArticleDOI
TL;DR: The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.
Abstract: MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.

3,388 citations

Journal ArticleDOI
01 Dec 1994-Yeast
TL;DR: A dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA is constructed and tested, and some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10–3–10–4.
Abstract: We have constructed and tested a dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA. This kanMX module contains the known kanr open reading-frame of the E. coli transposon Tn903 fused to transcriptional and translational control sequences of the TEF gene of the filamentous fungus Ashbya gossypii. This hybrid module permits efficient selection of transformants resistant against geneticin (G418). We also constructed a lacZMT reporter module in which the open reading-frame of the E. coli lacZ gene (lacking the first 9 codons) is fused at its 3' end to the S. cerevisiae ADH1 terminator. KanMX and the lacZMT module, or both modules together, were cloned in the center of a new multiple cloning sequence comprising 18 unique restriction sites flanked by Not I sites. Using the double module for constructions of in-frame substitutions of genes, only one transformation experiment is necessary to test the activity of the promotor and to search for phenotypes due to inactivation of this gene. To allow for repeated use of the G418 selection some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10(-3)-10(-4). The 1.4 kb kanMX module was also shown to be very useful for PCR based gene disruptions. In an experiment in which a gene disruption was done with DNA molecules carrying PCR-added terminal sequences of only 35 bases homology to each target site, all twelve tested geneticin-resistant colonies carried the correctly integrated kanMX module.

2,727 citations

Journal ArticleDOI
TL;DR: This review encompasses different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.
Abstract: The budding yeast Saccharomyces cerevisiae has been the principal organism used in experiments to examine genetic recombination in eukaryotes. Studies over the past decade have shown that meiotic recombination and probably most mitotic recombination arise from the repair of double-strand breaks (DSBs). There are multiple pathways by which such DSBs can be repaired, including several homologous recombination pathways and still other nonhomologous mechanisms. Our understanding has also been greatly enriched by the characterization of many proteins involved in recombination and by insights that link aspects of DNA repair to chromosome replication. New molecular models of DSB-induced gene conversion are presented. This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.

2,175 citations

Journal ArticleDOI
TL;DR: Four areas have seen major progress in the TGF-p superfamily in the last 3 years: structural characterization of the signal­ ing molecule, isolation of new family members, cloning of receptor molecules, and new genetic tests of the func­ tions of these factors in different organisms.
Abstract: In the last 10 years, a large family of secreted signaling molecules has been discovered that appear to mediate many key events in normal growth and development. The family is known as the TGF-p superfamily (Massague 1990), a name taken from the first member of the family to be isolated (transforming growth factor-^l). This name is somewhat misleading, because TGF-p 1 has a large number of effects in different systems (Spom and Roberts 1992). It actually inhibits the proliferation of many different cell lines, and its original "transforming" activity may be due to secondary effects on matrix pro­ duction and synthesis of other growth factors (Moses et al. 1990). The two dozen other members of the TGF-p superfamily have a remarkable range of activities. In Diosophila, a TGF-p-related gene is required for dorsoventral axis formation in early embryos, communication between tissue layers in gut development, and correct proximal distal patterning of adult appendages. In Xenopus, a TGF-p-related gene is expressed specifically at one end of fertilized eggs and may function in early signaling events that lay out the basic body plan. In mammals, TGF-p-related molecules have been found that control sexual development, pituitary hormone production, and the creation of bones and cartilage. The recognition of TGF-p superfamily members in many different organ­ isms and contexts provides one of the major unifying themes in recent molecular studies of animal growth and development. The rough outlines of the TGF-p family were first rec­ ognized in the 1980s. Since that time, a number of ex­ cellent reviews have appeared that summarize the prop­ erties of different family members (Ying 1989; Massague 1990; Lyons et al. 1991; Spom and Roberts 1992). Here, I will focus on four areas that have seen major progress in the last 3 years: structural characterization of the signal­ ing molecule, isolation of new family members, cloning of receptor molecules, and new genetic tests of the func­ tions of these factors in different organisms.

2,092 citations