- The structure of haplotype blocks in the human genome
Stacey B Gabriel
Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002
..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- Genome maintenance mechanisms for preventing cancer
J H Hoeijmakers
MGC Department of Cell Biology and Genetics, Centre for Biomedical Genetics, Erasmus University, PO Box 1738, 3000DR Rotterdam, The Netherlands
Nature 411:366-74. 2001
..This review summarizes the main DNA caretaking systems and their impact on genome stability and carcinogenesis...
- Mauve: multiple alignment of conserved genomic sequence with rearrangements
Aaron C E Darling
Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genome Res 14:1394-403. 2004
..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
- Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus
Department of Genetics and Development, Columbia University, New York, USA
BMC Dev Biol 1:4. 2001
- A simple and robust statistical test for detecting the presence of recombination
Trevor C Bruen
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
Genetics 172:2665-81. 2006
..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
- Evaluation of methods for detecting recombination from DNA sequences: computer simulations
Department of Zoology, Brigham Young University, Provo, UT 84602, USA
Proc Natl Acad Sci U S A 98:13757-62. 2001
..Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand...
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints
D P Martin
Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
AIDS Res Hum Retroviruses 21:98-102. 2005
- Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Science 300:1542-8. 2003
..Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling...
- Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003
..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
- Simple and highly efficient BAC recombineering using galK selection
Mouse Cancer Genetics Program, National Cancer Institute Frederick, MD 21702 1201, USA
Nucleic Acids Res 33:e36. 2005
- Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
M J Gibbs
Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia
Bioinformatics 16:573-82. 2000
..To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals...
- Generating samples under a Wright-Fisher neutral model of genetic variation
Richard R Hudson
Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
Bioinformatics 18:337-8. 2002
..The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models...
- Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
Dev Biol 244:305-18. 2002
..This inducible Cre system will be a broadly useful tool to modulate gene activity in mouse embryos, adults, and culture systems where temporal control is an important consideration...
- Sex and virulence in Escherichia coli: an evolutionary perspective
Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
Mol Microbiol 60:1136-51. 2006
..This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response...
- An exact nonparametric method for inferring mosaic structure in sequence triplets
Maciej F Boni
Stanford Genome Technology Center, Palo Alto, California 94304, USA
Genetics 176:1035-47. 2007
- A second generation human haplotype map of over 3.1 million SNPs
Kelly A Frazer
The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
Nature 449:851-61. 2007
..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
- An efficient recombination system for chromosome engineering in Escherichia coli
Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 97:5978-83. 2000
..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
- Regulation of DNA double-strand break repair pathway choice
Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine and Cancer Center, Albuquerque, NM 87131, USA
Cell Res 18:134-47. 2008
- Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31
Amy C Groth
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Genetics 166:1775-82. 2004
..These experiments demonstrate the potential for precise genetic engineering of the Drosophila genome with the phiC31 integrase system and will likely benefit research in Drosophila and other insects...
- XRCC3 promotes homology-directed repair of DNA damage in mammalian cells
A J Pierce
Cell Biology Program, Memorial Sloan Kettering Cancer Center and Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
Genes Dev 13:2633-8. 1999
..These results establish that XRCC3-mediated homologous recombination can reverse DNA damage that would otherwise be mutagenic or lethal...
- A highly efficient recombineering-based method for generating conditional knockout mutations
Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
Genome Res 13:476-84. 2003
..This method should also facilitate the generation of knock-in mutations and transgene constructs, as well as expedite the analysis of regulatory elements and functional domains in or near genes...
- CtIP-BRCA1 modulates the choice of DNA double-strand-break repair pathway throughout the cell cycle
Maximina H Yun
Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Nature 459:460-3. 2009
- Mechanism and regulation of class switch recombination
Department of Molecular Genetics and Microbiology, Program in Immunology and Virology, University of Massachusetts Medical School, Worcester, Massachusetts 01655 012, USA
Annu Rev Immunol 26:261-92. 2008
..These proteins are important for faithful joining of S regions, and in their absence aberrant recombination and chromosomal translocations involving S regions occur...
- A common sequence motif associated with recombination hot spots and genome instability in humans
Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 40:1124-9. 2008
- Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Genome Biol 8:R71. 2007
..This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts...
- Genome-wide insertional mutagenesis of Arabidopsis thaliana
Jose M Alonso
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
Science 301:653-7. 2003
..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
- GARD: a genetic algorithm for recombination detection
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
Bioinformatics 22:3096-8. 2006
..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
- Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme
Department of Medical Chemistry, Graduate School of Medicine, Institute for Virus Research, Kyoto University, Japan
Cell 102:553-63. 2000
..These results suggest that AID may be involved in regulation or catalysis of the DNA modification step of both class switching and somatic hypermutation...
- A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation
A R Templeton
Department of Biology, Washington University, St Louis, Missouri 63130
Genetics 132:619-33. 1992
..We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination...
- Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map
Hans van Os
Laboratory of Plant Breeding, Wageningen University, The Netherlands
Genetics 173:1075-87. 2006
- Paired-end mapping reveals extensive structural variation in the human genome
Jan O Korbel
Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
Science 318:420-6. 2007
..The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans...
- Systematic genetic analysis with ordered arrays of yeast deletion mutants
A H Tong
Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6
Science 294:2364-8. 2001
..Systematic application of this approach should produce a global map of gene function...
- Identification of Holliday junction resolvases from humans and yeast
Stephen C Y Ip
Genetic Recombination Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
Nature 456:357-61. 2008
..Recombinant GEN1 and Yen1 resolve Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated...
- Human CtIP promotes DNA end resection
Alessandro A Sartori
The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
Nature 450:509-14. 2007
..These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination...
- Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 7260, USA
Annu Rev Biochem 73:39-85. 2004
..In this review the molecular mechanisms of DNA repair and the DNA damage checkpoints in mammalian cells are analyzed...
- P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster
Koen J T Venken
Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
Science 314:1747-51. 2006
..This transgenesis platform should greatly facilitate structure/function analyses of most Drosophila genes...
- A fine-scale map of recombination rates and hotspots across the human genome
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Science 310:321-4. 2005
- RTEL1 maintains genomic stability by suppressing homologous recombination
Louise J Barber
DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
Cell 135:261-71. 2008
..We propose that loss of HR control after deregulation of RTEL1 may be a critical event that drives genome instability and cancer...
- Role of Mre11 in chromosomal nonhomologous end joining in mammalian cells
Unité mixte de recherche 217, Centre National de la Recherche Scientifique Commissariat à l Energie Atomique, Equipe labellisée LA LIGUE 2008, Institut de Radiobiologie Cellulaire et Moleculaire, Fontenay aux Roses, France
Nat Struct Mol Biol 16:819-24. 2009
..These data demonstrate that, in addition to its role in ATM activation, Mre11 can favor alternative NHEJ through its nuclease activity...
- Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination
Departamento de Genetica, Facultad de Biologia, Universidad de Sevilla, Avenida Reina, Mercedes 6, 41012 Seville, Spain
Mol Cell 12:711-21. 2003
..These data support a model to explain the connection between recombination, transcription, and mRNA metabolism and provide a new perspective to understanding transcription-associated recombination...
- Mechanism of eukaryotic homologous recombination
Joseph San Filippo
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
Annu Rev Biochem 77:229-57. 2008
..Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here...
- Detecting a local signature of genetic hitchhiking along a recombining chromosome
Department of Evolutionary Biology, University of Munich, 80333 Munich, Germany
Genetics 160:765-77. 2002
..This method also allows us to estimate the strength and the location of directional selection from DNA sequence data...
- Recombination and linkage disequilibrium in Arabidopsis thaliana
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Nat Genet 39:1151-5. 2007
..LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms...
- Mobile elements: drivers of genome evolution
Haig H Kazazian
Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Science 303:1626-32. 2004
..Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function...
- Highly efficient endogenous human gene correction using designed zinc-finger nucleases
Fyodor D Urnov
Sangamo BioSciences, Inc, Pt Richmond Tech Center 501, Canal Blvd, Suite A100 Richmond, California 94804, USA
Nature 435:646-51. 2005
..We observe comparably high frequencies in human T cells, raising the possibility of strategies based on zinc-finger nucleases for the treatment of disease...
- Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites
Institut Curie Centre de Recherche, UMR7147 CNRS, Universite Pierre et Marie Curie, Paris, France
EMBO J 28:99-111. 2009
..Novel perspectives to dissect the various layers of the controls of meiotic DSB formation are discussed...
- The genome of the African trypanosome Trypanosoma brucei
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Science 309:416-22. 2005
..brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified...
- RDP2: recombination detection and analysis from sequence alignments
D P Martin
Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town 7000, South Africa
Bioinformatics 21:260-2. 2005
- DNA double-strand break repair: from mechanistic understanding to cancer treatment
Radiation Oncology and Biology, University of Oxford, Oxford OX3 7LJ, UK
DNA Repair (Amst) 6:923-35. 2007
- An evolutionary view of human recombination
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 8:23-34. 2007
- Recombination patterns in aphthoviruses mirror those found in other picornaviruses
Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa
J Virol 80:11827-32. 2006
- High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
H M Ellis
Gene Regulation and Chromosome Biology Laboratory, Division of Basic Sciences, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 98:6742-6. 2001
..Beta protein and ssDNA may prove generally applicable for repairing DNA in many organisms...
- The origins of genome complexity
Department of Biology, Indiana University, Bloomington, IN 47405, USA
Science 302:1401-4. 2003
..The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies...
- A simplified system for generating recombinant adenoviruses
T C He
The Howard Hughes Medical Institute, 424 North Bond Street, Baltimore, MD 21231, USA
Proc Natl Acad Sci U S A 95:2509-14. 1998
..Homogeneous viruses can be obtained from this procedure without plaque purification. This system should expedite the process of generating and testing recombinant adenoviruses for a variety of purposes...
- Human DNA repair genes
R D Wood
Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
Science 291:1284-9. 2001
..Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process...
- Hybrid origin of SIV in chimpanzees
University of Nottingham, Nottingham NG72UH, UK
Science 300:1713. 2003
- Nonhomologous end joining in yeast
James M Daley
Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan 48109 0602, USA
Annu Rev Genet 39:431-51. 2005
..We also consider how the balance between NHEJ and homologous repair is regulated by cell state to promote genome preservation. The principles discussed are instructive to NHEJ in all organisms...
- Pathways of DNA double-strand break repair during the mammalian cell cycle
Fachrichtung Biophysik, Universitat des Saarlandes, D 66421 Homburg Saar, Germany
Mol Cell Biol 23:5706-15. 2003
..These data provide the first evaluation of the cell cycle-specific contributions of NHEJ and HR to the repair of radiation-induced versus replication-associated DSBs...
- Genome sequence of the human malaria parasite Plasmodium falciparum
Malcolm J Gardner
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nature 419:498-511. 2002
..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
- Transgeneration memory of stress in plants
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nature 442:1046-9. 2006
..We conclude that environmental factors lead to increased genomic flexibility even in successive, untreated generations, and may increase the potential for adaptation...
- Chk2 phosphorylation of BRCA1 regulates DNA double-strand break repair
Department of Radiation Oncology, Massachusetts General Hospital Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
Mol Cell Biol 24:708-18. 2004
..We propose a dual regulatory role for BRCA1 in maintaining genome integrity, whereby BRCA1 phosphorylation status controls the selectivity of repair events dictated by HR and error-prone NHR...
- DNA double-strand breaks: signaling, repair and the cancer connection
K K Khanna
The Queensland Institute of Medical Research, and Department of Pathology, University of Queensland, PO Royal Brisbane Hospital, Brisbane, Queensland, Australia
Nat Genet 27:247-54. 2001
..Moreover, we discuss how tumor suppressor proteins such as p53, ATM, Brca1 and Brca2 have been linked to such pathways, and how accumulating evidence is connecting deficiencies in cellular responses to DNA DSBs with tumorigenesis...
- The cell-cycle checkpoint kinase Chk1 is required for mammalian homologous recombination repair
Claus Storgaard Sørensen
Danish Cancer Society, Institute of Cancer Biology, DK 2100 Copenhagen, Denmark
Nat Cell Biol 7:195-201. 2005
..These results highlight a crucial role for the Chk1 signalling pathway in protecting cells against lethal DNA lesions through regulation of HRR...
- Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks
Wael Y Mansour
Laboratory of Radiobiology and Experimental Radiation Oncology, Department of Radiotherapy and Radiation Oncology, University Medical School Hamburg Eppendorf, Martinistrasse 52, D 20246 Hamburg, Germany
Nucleic Acids Res 36:4088-98. 2008
..Furthermore, the cellular choice of repair pathways is reversible and can be influenced at the level of effector proteins such as Ku80 or Rad51...
- Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites
Francene J Lemoine
Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Cell 120:587-98. 2005
..We demonstrate that this pair of Ty elements constitutes a preferred site for double-strand DNA breaks when DNA replication is compromised, analogous to the fragile sites observed in mammalian chromosomes...
- Distinct histone modifications define initiation and repair of meiotic recombination in the mouse
Institut de Genetique Humaine, CNRS UPR 1142, Montpellier, France
EMBO J 28:2616-24. 2009
..Altogether, the chromatin signatures of the Psmb9 and Hlx1 hotspots provide a basis for understanding the distribution of meiotic recombination...
- Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae
S J Lin
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 289:2126-8. 2000
..These findings suggest that the increased longevity induced by calorie restriction requires the activation of Sir2p by NAD...
- Automated phylogenetic detection of recombination using a genetic algorithm
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, USA
Mol Biol Evol 23:1891-901. 2006
..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection...
- Mating-type gene switching in Saccharomyces cerevisiae
J E Haber
Department of Biology, Brandeis University, Waltham, Massachusetts 02454 9110, USA
Annu Rev Genet 32:561-99. 1998
..In addition, MAT switching provides a remarkable example of a small locus control region--the Recombination Enhancer--that controls recombination along an entire chromosome arm...
- Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system
Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
Nature 450:56-62. 2007
..The ability of the Brainbow system to label uniquely many individual cells within a population may facilitate the analysis of neuronal circuitry on a large scale...
- The SOS response controls integron recombination
Universite de Limoges, Faculte de Medecine, EA3175, INSERM, Equipe Avenir, 87000 Limoges, France
Science 324:1034. 2009
..This finding exposes integrons as integrated adaptive systems and has implications for antibiotic treatment policies...
- Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
Mamie Z Li
Howard Hughes Medical Institute, Department of Genetics, Harvard Partners Center for Genetics and Genomics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Nat Methods 4:251-6. 2007
..This flexibility allows much greater versatility in the generation of recombinant DNA for the purposes of synthetic biology...
- Modification of gene activity in mouse embryos in utero by a tamoxifen-inducible form of Cre recombinase
P S Danielian
Department of Molecular and Cellular Biology Harvard University 16 Divinity Avenue, Cambridge Massachusetts 02138 USA
Curr Biol 8:1323-6. 1998
..Induction was ligand dependent, rapid and efficient. The results demonstrate that tamoxifen-inducible recombination can be used to effectively modify gene function in the mouse embryo...
- Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases
Genome Instability and Carcinogenesis UPR3081 CNRS, Conventionné par l Université d Aix Marseille 2, IGC, IMM 31 chemin Joseph Aiguier, 13402 Marseille, France
Cell 138:78-89. 2009
..We propose that SLX4 acts as a docking platform for multiple structure-specific endonucleases...
- Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase
Louis J Nkrumah
Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
Nat Methods 3:615-21. 2006
..falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms...
- RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination
M A Oettinger
Whitehead Institute for Biomedical Research, Cambridge, MA 02142
Science 248:1517-23. 1990
..RAG-1 and RAG-2 might activate the expression of the V(D)J recombinase but, more likely, they directly participate in the recombination reaction...
- Chromosome sites play dual roles to establish homologous synapsis during meiosis in C. elegans
Amy J MacQueen
Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Cell 123:1037-50. 2005
..We speculate that concentration of these activities at one region per chromosome may have coevolved with the loss of a point centromere to safeguard karyotype stability...
- The complete genome sequence of the gastric pathogen Helicobacter pylori
J F Tomb
Institute for Genomic Research, Rockville, Maryland 20850, USA
Nature 388:539-47. 1997
..pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH...
- Conditional control of gene expression in the mouse
Section of Genetics of Vertebrate Development, Laboratory of Cancer and Developmental Biology, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, Maryland 21702 1201, USA
Nat Rev Genet 2:743-55. 2001
..Here, I review these systems and discuss certain studies that exemplify the advantages and limitations of each system...
- The Bloom's syndrome gene product promotes branch migration of holliday junctions
J K Karow
Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
Proc Natl Acad Sci U S A 97:6504-8. 2000
..We present a model in which BLM disrupts potentially recombinogenic molecules that arise at sites of stalled replication forks. Our results have implications for the role of BLM as an anti-recombinase in the suppression of tumorigenesis...
- The recombinational anatomy of a mouse chromosome
Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
PLoS Genet 4:e1000119. 2008
Among mammals, genetic recombination occurs at highly delimited sites known as recombination hotspots. They are typically 1-2 kb long and vary as much as a 1,000-fold or more in recombination activity...
- The endless tale of non-homologous end-joining
Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center, 2201 Inwood Road, Dallas, TX 75390 9187, USA
Cell Res 18:114-24. 2008
..In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented...
- A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes
CRBM, CNRS FRE2593, 1919 Route de Mende, F 34293 Montpellier cedex 5, France
Yeast 21:947-62. 2004
..This new toolbox should help to speed up the analysis of gene function in yeast, on the level of single genes, as well as in systematic approaches...
- Mechanism of genetic exchange in American trypanosomes
Michael W Gaunt
Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
Nature 421:936-9. 2003
..cruzi. In this instance, aneuploidy through nuclear hybridization results in recombination across far greater genetic distances than mendelian genetic exchange. This mechanism also parallels genome duplication...
- A recalibrated molecular clock and independent origins for the cholera pandemic clones
TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
PLoS ONE 3:e4053. 2008
..The approaches used open up new avenues for analysing the origin and history of other important pathogens...
- Frequency and dynamics of recombination within different species of human enteroviruses
Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
J Virol 80:483-93. 2006
- Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy
Cellectis SA, 102, route de Noisy, 93 340 Romainville Cedex France
Curr Gene Ther 7:49-66. 2007
..Finally, we will discuss the main issues that will need to be addressed in order to bring this promising technology to the patient...
- Targeted disruption of the c-src proto-oncogene leads to osteopetrosis in mice
Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030
Cell 64:693-702. 1991
..These results demonstrate that src is not required for general cell viability (possibly because of functional overlap with other tyrosine kinases related to src) and uncover an essential role for src in bone formation...
- The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease
Najib M El-Sayed
Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA
Science 309:409-15. 2005
- A high-resolution single nucleotide polymorphism genetic map of the mouse genome
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
PLoS Biol 4:e395. 2006
..Genetic maps are available from http://gscan.well.ox.ac.uk/#genetic_map and as supporting information to this publication...
- Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination
Medical Genetics Center, Department of Cell Biology and Genetics, Erasmus University Rotterdam, The Netherlands
Cell 89:195-204. 1997
..Thus, mRAD54 is not required for the recombination processes that generate functional immunoglobulin and T cell receptor genes...
- Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution
John A Birdsell
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85121, USA
Mol Biol Evol 19:1181-97. 2002
..These findings have a number of important implications for the way we view genome evolution and suggest a new model for the evolution of sex...
- A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
Martien A M Groenen
Animal Breeding and Genomics Centre, Wageningen University, 6700 AH Wageningen, The Netherlands
Genome Res 19:510-9. 2009
..4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding...
- A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA
Committee on Genetics, University of Chicago, Illinois 60637
Cell 56:771-6. 1989
..Here we demonstrate that SIR2's effect is not restricted to controlling mating type expression, but rather that SIR2 functions in a more general way in the genome...
- The consequences of Rad51 overexpression for normal and tumor cells
Hannah L Klein
Department of Biochemistry, New York University School of Medicine, NYU Medical Center, 550 First Avenue, New York, NY 10016, United States
DNA Repair (Amst) 7:686-93. 2008
..While increased Rad51 can provide drug resistance, it also leads to increased genomic instability and may contribute to carcinogenesis...
- Pervasive hitchhiking at coding and regulatory sites in humans
James J Cai
Department of Biology, Stanford University, Stanford, CA, USA
PLoS Genet 5:e1000336. 2009
..These findings suggest that the effects of natural selection at linked sites cannot be ignored in the study of neutral human polymorphism...
- BRCA2: a universal recombinase regulator
London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts, UK
Oncogene 26:7720-30. 2007
..The interactions of BRCA2 with RAD51 and DMC1 lead us to suggest that the BRCA2 tumour suppressor is a universal regulator of recombinase actions...
- 53BP1 facilitates long-range DNA end-joining during V(D)J recombination
Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 1360, USA
Nature 456:529-33. 2008
..These data suggest a more general role for 53BP1 in maintaining genomic stability during long-range joining of DNA breaks...
- Mechanism of homologous recombination: mediators and helicases take on regulatory functions
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
Nat Rev Mol Cell Biol 7:739-50. 2006
..Defects in BLM are also associated with the cancer phenotype. The past several years have witnessed dramatic advances in our understanding of the mechanism and regulation of HR...
- Evidence of recombination among enteroviruses
MediCity Research Laboratory and Department of Virology, University of Turku, FIN 20520 Turku, National Public Health Institute, FIN 00300 Helsinki, Finland
J Virol 73:8741-9. 1999
..Recombination breakpoints were detected in all genomic regions except the capsid protein coding region. Our results suggest that recombination is a significant and relatively frequent mechanism in the evolution of enterovirus genomes...