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Bernard Dujon

Bio: Bernard Dujon is an academic researcher from Pasteur Institute. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 70, co-authored 189 publications receiving 22915 citations. Previous affiliations of Bernard Dujon include Centre national de la recherche scientifique & Pierre-and-Marie-Curie University.


Papers
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Journal ArticleDOI
25 Oct 1996-Science
TL;DR: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration and provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history.
Abstract: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

4,254 citations

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
Stephen G. Oliver1, Q. J. M. van der Aart2, M. L. Agostoni-Carbone3, Michel Aigle, Lilia Alberghina3, Despina Alexandraki, G. Antoine4, Rashida Anwar1, Juan P. G. Ballesta, Paule Bénit4, Gilbert Berben, Elisabetta Bergantino, N. Biteau, P. A. Bolle, Monique Bolotin-Fukuhara5, Anthony G. A. Brown1, Alistair J. P. Brown6, J. M. Buhler, C. Carcano3, Giovanna Carignani, Håkan Cederberg, R. Chanet4, Roland Contreras, Marc Crouzet, B. Daignan-Fornier5, E. Defoor7, M. Delgado, Jan Demolder, C. Doira5, Evelyne Dubois, Bernard Dujon8, A. Düsterhöft, D. Erdmann, M. Esteban, F. Fabre4, Cécile Fairhead8, Gérard Faye4, Horst Feldmann9, Walter Fiers, M. C. Francingues-Gaillard5, L. Franco, Laura Frontali10, H. Fukuhara4, L. J. Fuller11, P. Galland, Manda E. Gent1, D. Gigot, Véronique Gilliquet, Glansdorff Nn, André Goffeau12, M. Grenson13, P. Grisanti10, Leslie A. Grivell14, M. de Haan14, M. Haasemann, D. Hatat15, Janet Hoenicka, Johannes H. Hegemann, C. J. Herbert16, François Hilger, Stefan Hohmann, Cornelis P. Hollenberg, K. Huse, F. Iborra5, K. J. Indje1, K. Isono17, C. Jacq15, M. Jacquet5, C. M. James1, J. C. Jauniaux13, Y. Jia16, Alberto Jiménez, A. Kelly18, U. Kleinhans, P Kreisl, G. Lanfranchi, C Lewis11, C. G. vanderLinden19, G Lucchini3, K Lutzenkirchen, M.J. Maat14, L. Mallet5, G. Mannhaupet9, Enzo Martegani3, A. Mathieu4, C. T. C. Maurer19, David J. McConnell18, R. A. McKee11, F. Messenguy, Hans-Werner Mewes, Francis Molemans, M. A. Montague18, M. Muzi Falconi3, L. Navas, Carol S. Newlon20, D. Noone18, C. Pallier5, L. Panzeri3, Bruce M. Pearson11, J. Perea15, Peter Philippsen, A. Pierard, Rudi J. Planta19, Paolo Plevani3, B. Poetsch, Fritz M. Pohl21, B. Purnelle12, M. Ramezani Rad, S. W. Rasmussen, A. Raynal5, Miguel Remacha, P. Richterich21, Aki Roberts6, F. Rodriguez3, E. Sanz, I. Schaaff-Gerstenschlager, Bart Scherens, Bertold Schweitzer, Y. Shu15, J. Skala12, Piotr P. Slonimski16, F. Sor4, C. Soustelle5, R. Spiegelberg, Lubomira Stateva1, H. Y. Steensma2, S. Steiner, Agnès Thierry8, George Thireos, Maria Tzermia, L. A. Urrestarazu13, Giorgio Valle, I. Vetter9, J. C. van Vliet-Reedijk19, Marleen Voet7, Guido Volckaert7, P. Vreken19, H. Wang18, John R. Warmington1, D. von Wettstein, Barton Luke Wicksteed6, C. Wilson10, H. Wurst21, G. Xu, A. Yoshikawa17, Friedrich K. Zimmermann, J. G. Sgouros 
07 May 1992-Nature
TL;DR: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined, which is the first complete sequence analysis of an entire chromosome from any organism.
Abstract: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

811 citations

Journal ArticleDOI
TL;DR: The bakers' yeast, Saccharomyces cerevisiae, a microorganism of major importance for bio industry, and one of the favored model organisms for basic biological research, is the first eukaryote whose genome is entirely sequenced as mentioned in this paper.

556 citations

Journal ArticleDOI
TL;DR: This paper showed that double-strand break repair can be initiated by the I-SceI endonuclease at a predetermined location in the mouse genome and that the breaks can be repaired with a donor molecule homologous regions flanking the breaks.
Abstract: The mitochondrial intron-encoded endonuclease I-SceI of Saccharomyces cerevisiae has an 18-bp recognition sequence and, therefore, has a very low probability of cutting DNA, even within large genomes. We demonstrate that double-strand breaks can be initiated by the I-SceI endonuclease at a predetermined location in the mouse genome and that the breaks can be repaired with a donor molecule homologous regions flanking the breaks. This induced homologous recombination is approximately 2 orders of magnitude more frequent than spontaneous homologous recombination and at least 10 times more frequent than random integration near an active promoter. As a consequence of induced homologous recombination, a heterologous novel sequence can be inserted at the site of the break. This recombination can occur at a variety of chromosomal targets in differentiated and multipotential cells. These results demonstrate homologous recombination involving chromosomal DNA by the double-strand break repair mechanism in mammals and show the usefulness of very rare cutter endonucleases, such as I-SceI, for designing genome rearrangements.

554 citations


Cited by
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Journal ArticleDOI
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Abstract: Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

35,225 citations

Journal ArticleDOI
Eric S. Lander1, Lauren Linton1, Bruce W. Birren1, Chad Nusbaum1  +245 moreInstitutions (29)
15 Feb 2001-Nature
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

22,269 citations

Journal ArticleDOI
J. Craig Venter1, Mark Raymond Adams1, Eugene W. Myers1, Peter W. Li1  +269 moreInstitutions (12)
16 Feb 2001-Science
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

12,098 citations

Journal ArticleDOI
05 Sep 1997-Science
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Abstract: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

7,723 citations

Journal ArticleDOI
10 Feb 2000-Nature
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
Abstract: Two large-scale yeast two-hybrid screens were undertaken to identify protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transformant expressing one of the open reading frames as a fusion to an activation domain. This array was screened by a simple and automated procedure for 192 yeast proteins, with positive responses identified by their positions in the array. In a second approach, we pooled cells expressing one of about 6,000 activation domain fusions to generate a library. We used a high-throughput screening procedure to screen nearly all of the 6,000 predicted yeast proteins, expressed as Gal4 DNA-binding domain fusion proteins, against the library, and characterized positives by sequence analysis. These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. These data reveal interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. The results of these screens are shown here.

4,877 citations