Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Science 5 September 1997:
Vol. 277. no. 5331, pp. 1518 - 1523
DOI: 10.1126/science.277.5331.1518

Reports

Dynamic Molecular Combing: Stretching the Whole Human Genome for High-Resolution Studies

Xavier Michalet, * Rosemary Ekong, * Françoise Fougerousse, Sophie Rousseaux, dagger Catherine Schurra, Nick Hornigold, Marjon van Slegtenhorst, Jonathan Wolfe, Sue Povey, Jacques S. Beckmann, Aaron Bensimon ddagger

DNA in amounts representative of hundreds of eukaryotic genomes was extended on silanized surfaces by dynamic molecular combing. The precise measurement of hybridized DNA probes was achieved directly without requiring normalization. This approach was validated with the high-resolution mapping of cosmid contigs on a yeast artificial chromosome (YAC) within yeast genomic DNA. It was extended to human genomic DNA for precise measurements ranging from 7 to 150 kilobases, of gaps within a contig, and of microdeletions in the tuberous sclerosis 2 gene on patients' DNA. The simplicity, reproducibility, and precision of this approach makes it a powerful tool for a variety of genomic studies.

X. Michalet, C. Schurra, A. Bensimon, Laboratoire de Biophysique de l'ADN, Département des Biotechnologies, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.
R. Ekong, S. Rousseaux, S. Povey, MRC Human Biochemical Genetics Unit, University College London, 4 Stephenson Way, London NW1 2HE, UK.
F. Fougerousse and J. S. Beckmann, URA 1922, Généthon, 1 rue de l'Internationale, Boîte Postale 60, 91002 Evry, France.
N. Hornigold and J. Wolfe, The Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK.
M. van Slegtenhorst, Department of Clinical Genetics, Erasmus University, Dr. Molewaterplein 50, NL-3015, GE Rotterdam, Netherlands.
*   These authors contributed equally to this work.

dagger    Present address: INSERM U309, Institut Albert Bonniot, 39706 La Tronche Cedex, France.

ddagger    To whom correspondence should be addressed. E-mail: abensim{at}pasteur.fr


Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Y RNA functions at the initiation step of mammalian chromosomal DNA replication.
T. Krude, C. P. Christov, O. Hyrien, and K. Marheineke (2009)
J. Cell Sci. 122, 2836-2845
   Abstract »    Full Text »    PDF »
Specific function of phosphoinositide 3-kinase beta in the control of DNA replication.
M. Marques, A. Kumar, A. M. Poveda, S. Zuluaga, C. Hernandez, S. Jackson, P. Pasero, and A. C. Carrera (2009)
PNAS 106, 7525-7530
   Abstract »    Full Text »    PDF »
Replication initiation complex formation in the absence of nuclear function in Xenopus.
L. Krasinska and D. Fisher (2009)
Nucleic Acids Res. 37, 2238-2248
   Abstract »    Full Text »    PDF »
Cyclin A-Cdk1 regulates the origin firing program in mammalian cells.
Y. Katsuno, A. Suzuki, K. Sugimura, K. Okumura, D. H. Zineldeen, M. Shimada, H. Niida, T. Mizuno, F. Hanaoka, and M. Nakanishi (2009)
PNAS 106, 3184-3189
   Abstract »    Full Text »    PDF »
PARP-1 ensures regulation of replication fork progression by homologous recombination on damaged DNA.
K. Sugimura, S.-i. Takebayashi, H. Taguchi, S. Takeda, and K. Okumura (2008)
J. Cell Biol. 183, 1203-1212
   Abstract »    Full Text »    PDF »
In Xenopus Egg Extracts, DNA Replication Initiates Preferentially at or near Asymmetric AT Sequences.
S. Stanojcic, J.-M. Lemaitre, K. Brodolin, E. Danis, and M. Mechali (2008)
Mol. Cell. Biol. 28, 5265-5274
   Abstract »    Full Text »    PDF »
A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments.
S. D. Sheridan, X. Yu, R. Roth, J. E. Heuser, M. G. Sehorn, P. Sung, E. H. Egelman, and D. K. Bishop (2008)
Nucleic Acids Res. 36, 4057-4066
   Abstract »    Full Text »    PDF »
Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication.
A. Ibarra, E. Schwob, and J. Mendez (2008)
PNAS 105, 8956-8961
   Abstract »    Full Text »    PDF »
A topoisomerase II-dependent mechanism for resetting replicons at the S-M-phase transition.
O. Cuvier, S. Stanojcic, J.-M. Lemaitre, and M. Mechali (2008)
Genes & Dev. 22, 860-865
   Abstract »    Full Text »    PDF »
Minichromosome Maintenance Proteins Interact with Checkpoint and Recombination Proteins To Promote S-Phase Genome Stability.
J. M. Bailis, D. D. Luche, T. Hunter, and S. L. Forsburg (2008)
Mol. Cell. Biol. 28, 1724-1738
   Abstract »    Full Text »    PDF »
A homologous recombination defect affects replication-fork progression in mammalian cells.
F. Daboussi, S. Courbet, S. Benhamou, P. Kannouche, M. Z. Zdzienicka, M. Debatisse, and B. S. Lopez (2008)
J. Cell Sci. 121, 162-166
   Abstract »    Full Text »    PDF »
PR-Set7 dependent lysine methylation ensures genome replication and stability through S phase.
M. Tardat, R. Murr, Z. Herceg, C. Sardet, and E. Julien (2007)
J. Cell Biol. 179, 1413-1426
   Abstract »    Full Text »    PDF »
Phosphorylation of Slx4 by Mec1 and Tel1 Regulates the Single-Strand Annealing Mode of DNA Repair in Budding Yeast.
S. Flott, C. Alabert, G. W. Toh, R. Toth, N. Sugawara, D. G. Campbell, J. E. Haber, P. Pasero, and J. Rouse (2007)
Mol. Cell. Biol. 27, 6433-6445
   Abstract »    Full Text »    PDF »
Replication Fork Velocities at Adjacent Replication Origins Are Coordinately Modified during DNA Replication in Human Cells.
C. Conti, B. Sacca, J. Herrick, C. Lalou, Y. Pommier, and A. Bensimon (2007)
Mol. Biol. Cell 18, 3059-3067
   Abstract »    Full Text »    PDF »
Endogenous {gamma}-H2AX-ATM-Chk2 Checkpoint Activation in Bloom's Syndrome Helicase Deficient Cells Is Related to DNA Replication Arrested Forks.
V. A. Rao, C. Conti, J. Guirouilh-Barbat, A. Nakamura, Z.-H. Miao, S. L. Davies, B. Sacca, I. D. Hickson, A. Bensimon, and Y. Pommier (2007)
Mol. Cancer Res. 5, 713-724
   Abstract »    Full Text »    PDF »
Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules.
J. H. Kim and R. G. Larson (2007)
Nucleic Acids Res. 35, 3848-3858
   Abstract »    Full Text »    PDF »
Anaphase Onset Before Complete DNA Replication with Intact Checkpoint Responses.
J. Torres-Rosell, G. De Piccoli, V. Cordon-Preciado, S. Farmer, A. Jarmuz, F. Machin, P. Pasero, M. Lisby, J. E. Haber, and L. Aragon (2007)
Science 315, 1411-1415
   Abstract »    Full Text »    PDF »
A simple DNA stretching method for fluorescence imaging of single DNA molecules.
T.-F. Chan, C. Ha, A. Phong, D. Cai, E. Wan, L. Leung, P.-Y. Kwok, and M. Xiao (2006)
Nucleic Acids Res. 34, e113
   Abstract »    Full Text »    PDF »
Proliferating Human Cells Hypomorphic for Origin Recognition Complex 2 and Pre-replicative Complex Formation Have a Defect in p53 Activation and Cdk2 Kinase Activation.
J. K. Teer, Y. J. Machida, H. Labit, O. Novac, O. Hyrien, K. Marheineke, M. Zannis-Hadjopoulos, and A. Dutta (2006)
J. Biol. Chem. 281, 6253-6260
   Abstract »    Full Text »    PDF »
DNA Replication Origins Fire Stochastically in Fission Yeast.
P. K. Patel, B. Arcangioli, S. P. Baker, A. Bensimon, and N. Rhind (2006)
Mol. Biol. Cell 17, 308-316
   Abstract »    Full Text »    PDF »
From the Cover: Generating highly ordered DNA nanostrand arrays.
J. Guan and L. J. Lee (2005)
PNAS 102, 18321-18325
   Abstract »    Full Text »    PDF »
Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system.
K. Marheineke, O. Hyrien, and T. Krude (2005)
Nucleic Acids Res. 33, 6931-6941
   Abstract »    Full Text »    PDF »
DNA Replication Origin Plasticity and Perturbed Fork Progression in Human Inverted Repeats.
R. Lebofsky and A. Bensimon (2005)
Mol. Cell. Biol. 25, 6789-6797
   Abstract »    Full Text »    PDF »
Human ribosomal RNA gene arrays display a broad range of palindromic structures.
S. Caburet, C. Conti, C. Schurra, R. Lebofsky, S. J. Edelstein, and A. Bensimon (2005)
Genome Res. 15, 1079-1085
   Abstract »    Full Text »    PDF »
Detection of single DNA molecules by multicolor quantum-dot end-labeling.
A. Crut, B. Geron-Landre, I. Bonnet, S. Bonneau, P. Desbiolles, and C. Escude (2005)
Nucleic Acids Res. 33, e98
   Abstract »    Full Text »    PDF »
Genomic Organization of Amplified MYC Genes Suggests Distinct Mechanisms of Amplification in Tumorigenesis.
J. Herrick, C. Conti, S. Teissier, F. Thierry, J. Couturier, X. Sastre-Garau, M. Favre, G. Orth, and A. Bensimon (2005)
Cancer Res. 65, 1174-1179
   Abstract »    Full Text »    PDF »
Nanometer-localized multiple single-molecule fluorescence microscopy.
X. Qu, D. Wu, L. Mets, and N. F. Scherer (2004)
PNAS 101, 11298-11303
   Abstract »    Full Text »    PDF »
Control of Replication Origin Density and Firing Time in Xenopus Egg Extracts: ROLE OF A CAFFEINE-SENSITIVE, ATR-DEPENDENT CHECKPOINT.
K. Marheineke and O. Hyrien (2004)
J. Biol. Chem. 279, 28071-28081
   Abstract »    Full Text »    PDF »
Sequence-specific fluorescent labeling of double-stranded DNA observed at the single molecule level.
B. Geron-Landre, T. Roulon, P. Desbiolles, and C. Escude (2003)
Nucleic Acids Res. 31, e125
   Abstract »    Full Text »    PDF »
Spatial distribution and specification of mammalian replication origins during G1 phase.
F. Li, J. Chen, E. Solessio, and D. M. Gilbert (2003)
J. Cell Biol. 161, 257-266
   Abstract »    Full Text »    PDF »
ORC and the intra-S-phase checkpoint: a threshold regulates Rad53p activation in S phase.
K. Shimada, P. Pasero, and S. M. Gasser (2002)
Genes & Dev. 16, 3236-3252
   Abstract »    Full Text »    PDF »
Bar code screening on combed DNA for large rearrangements of the BRCA1 and BRCA2 genes in French breast cancer families.
S Gad, M Klinger, V Caux-Moncoutier, S Pages-Berhouet, M Gauthier-Villars, I Coupier, A Bensimon, A Aurias, and D Stoppa-Lyonnet (2002)
J. Med. Genet. 39, 817-821
   Full Text »    PDF »
Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus.
P. Pasero, A. Bensimon, and E. Schwob (2002)
Genes & Dev. 16, 2479-2484
   Abstract »    Full Text »    PDF »
Observation by fluorescence microscopy of transcription on single combed DNA.
Z. Gueroui, C. Place, E. Freyssingeas, and B. Berge (2002)
PNAS 99, 6005-6010
   Abstract »    Full Text »    PDF »
Visualization of DNA Replication on Individual Epstein-Barr Virus Episomes.
P. Norio and C. L. Schildkraut (2001)
Science 294, 2361-2364
   Abstract »    Full Text »    PDF »
Behavior of DNA fibers stretched by precise meniscus motion control.
K. Otobe and T. Ohtani (2001)
Nucleic Acids Res. 29, e109
   Abstract »    Full Text »    PDF »
DNA Fiber Mapping Techniques for the Assembly of High-resolution Physical Maps.
H.-U. G. Weier (2001)
J. Histochem. Cytochem. 49, 939-948
   Abstract »    Full Text »    PDF »
Identification of a large rearrangement of the BRCA1 gene using colour bar code on combed DNA in an American breast/ovarian cancer family previously studied by direct sequencing.
S. Gad, M. T Scheuner, S. Pages-Berhouet, V. Caux-Moncoutier, A. Bensimon, A. Aurias, M. Pinto, and D. Stoppa-Lyonnet (2001)
J. Med. Genet. 38, 388-392
   Full Text »
Monitoring S phase progression globally and locally using BrdU incorporation in TK+ yeast strains.
A. Lengronne, P. Pasero, A. Bensimon, and E. Schwob (2001)
Nucleic Acids Res. 29, 1433-1442
   Abstract »    Full Text »    PDF »
Characterisation of six large deletions in TSC2 identified using long range PCR suggests diverse mechanisms including Alu mediated recombination.
S L DABORA, A A NIETO, D FRANZ, S JOZWIAK, A VAN DEN OUWELAND, and D J KWIATKOWSKI (2000)
J. Med. Genet. 37, 877-883
   Full Text »
DNA Fiber-FISH Staining Mechanism.
F. M. van de Rijke, R. J. Florijn, H. J. Tanke, and A. K. Raap (2000)
J. Histochem. Cytochem. 48, 743-746
   Abstract »    Full Text »
Encephalitozoon cuniculi (Microspora) genome: physical map and evidence for telomere-associated rDNA units on all chromosomes.
J.-F. Brugere, E. Cornillot, G. Metenier, A. Bensimon, and C. P. Vivares (2000)
Nucleic Acids Res. 28, 2026-2033
   Abstract »    Full Text »    PDF »
Quantifying single gene copy number by measuring fluorescent probe lengths on combed genomic DNA.
J. Herrick, X. Michalet, C. Conti, C. Schurra, and A. Bensimon (2000)
PNAS 97, 222-227
   Abstract »    Full Text »    PDF »
Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules.
J. Jing, J. Reed, J. Huang, X. Hu, V. Clarke, J. Edington, D. Housman, T. S. Anantharaman, E. J. Huff, B. Mishra, et al. (1998)
PNAS 95, 8046-8051
   Abstract »    Full Text »    PDF »
Use of a Mycobacterium tuberculosis H37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics.
R. Brosch, S. V. Gordon, A. Billault, T. Garnier, K. Eiglmeier, C. Soravito, B. G. Barrell, and S. T. Cole (1998)
Infect. Immun. 66, 2221-2229
   Abstract »    Full Text »    PDF »
Aphidicolin Triggers a Block to Replication Origin Firing in Xenopus Egg Extracts.
K. Marheineke and O. Hyrien (2001)
J. Biol. Chem. 276, 17092-17100
   Abstract »    Full Text »    PDF »



To Advertise     Find Products


Science. ISSN 0036-8075 (print), 1095-9203 (online)