- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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
- 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...
- 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...
- Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing
Eleni P Mimitou
Department of Microbiology, Columbia University Medical Center, 701 West 168th Street, New York, New York 10032, USA
Nature 455:770-4. 2008
..Second, Exo1 and/or Sgs1 rapidly process this intermediate to generate extensive tracts of single-stranded DNA that serve as substrate for Rad51...
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- Crossover/noncrossover differentiation, synaptonemal complex formation, and regulatory surveillance at the leptotene/zygotene transition of meiosis
G Valentin Börner
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Cell 117:29-45. 2004
- 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
- Inducible gene targeting in mice
Institute for Genetics, University of Cologne, Germany
Science 269:1427-9. 1995
..Deletion was complete in liver and nearly complete in lymphocytes within a few days, whereas partial deletion was obtained in other tissues. This method can be used for the inducible inactivation of any other gene in vivo...
- 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...
- 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...
- 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...
- 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...
- Un ménage à quatre: the molecular biology of chromosome segregation in meiosis
Research Institute of Molecular Pathology, Dr Bohrgasse 7, 1030 Vienna, Austria
Cell 112:423-40. 2003
- DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression
D K Bishop
Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
Cell 69:439-56. 1992
..DMC1 is homologous to yeast's RAD51 gene, supporting the view that mitotic DSB repair has been recruited for use in meiotic chromosome metabolism...
- The Collaborative Cross, a community resource for the genetic analysis of complex traits
Gary A Churchill
The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
Nat Genet 36:1133-7. 2004
..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...
- To err (meiotically) is human: the genesis of human aneuploidy
Department of Genetics, Case Western Reserve University, 10, 900 Euclid Avenue, Cleveland, Ohio 44106, USA
Nat Rev Genet 2:280-91. 2001
..However, recent molecular and cytogenetic approaches are now beginning to shed light on the non-disjunctional processes that lead to aneuploidy...
- DNA cloning using in vitro site-specific recombination
J L Hartley
Life Technologies, Inc, Rockville, Maryland 20850, USA
Genome Res 10:1788-95. 2000
..In this paper, we outline the concepts of this approach and provide several examples that highlight some of its potential...
- Meiotic chromosomes: integrating structure and function
Institut de Genetique et Microbiologie, Universite Paris Sud, Orsay, France
Annu Rev Genet 33:603-754. 1999
..The current article reviews recent information on these topics in an historical context. This juxtaposition has suggested new relationships between structure and function. Additional issues were addressed in a previous chapter (551)...
- 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 coalescent-based method for detecting and estimating recombination from gene sequences
Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
Genetics 160:1231-41. 2002
..The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data...
- 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...
- Hitchhiking under positive Darwinian selection
J C Fay
Committee on Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genetics 155:1405-13. 2000
..Application of the H test to published surveys of Drosophila variation reveals an excess of high frequency variants that are likely to have been influenced by positive selection...
- 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...
- 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...
- 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
- Differential timing and control of noncrossover and crossover recombination during meiosis
Laboratory of Biochemistry, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Cell 106:47-57. 2001
..These results suggest that crossovers are formed by resolution of Holliday junction intermediates, while most noncrossover recombinants arise by a different, earlier pathway...
- 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
- Mechanisms of site-specific recombination
Nigel D F Grindley
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
Annu Rev Biochem 75:567-605. 2006
..Details of the site-specific recombination processes have been revealed by recent structural and biochemical studies of members of both families...
- 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...
- Talking about a revolution: The impact of site-specific recombinases on genetic analyses in mice
Catherine S Branda
Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Dev Cell 6:7-28. 2004
..By enabling high-fidelity DNA modifications to be induced in vitro or in vivo, these systems have incited a wave of new biology, advancing our understanding of gene function, genetic relationships, development, and disease...
- 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...
- Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein
Department of Biology, Faculty of Science, Osaka University, Japan
Cell 69:457-70. 1992
..Rad51 protein is also homologous to a meiosis-specific Dmc1 protein of S. cerevisiae...
- The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination
Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
Cell 106:59-70. 2001
..This feature can explain crossover suppression between homeologous and structurally heterozygous chromosomes...
- The effect of recombination on the accuracy of phylogeny estimation
Department of Zoology, Brigham Young University, Provo, UT 84602, USA
J Mol Evol 54:396-402. 2002
..In this case, when the recombinational breakpoint divided the alignment in two regions of similar length, a phylogeny that was different from any of the true phylogenies underlying the data was inferred...
- 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...
- 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
- 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...
- Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects
Jose M Sogo
Institute of Cell Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
Science 297:599-602. 2002
..We speculate that, in checkpoint mutants, abnormal replication intermediates begin to form because of uncoordinated replication and are further processed by unscheduled recombination pathways, causing genome instability...
- Four evolutionary strata on the human X chromosome
B T Lahn
Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 286:964-7. 1999
..The first event, which marked the beginnings of X-Y differentiation, occurred about 240 to 320 million years ago, shortly after divergence of the mammalian and avian lineages...
- Ubc9- and mms21-mediated sumoylation counteracts recombinogenic events at damaged replication forks
FIRC Institute of Molecular Oncology Foundation and Department of Biomedical Sciences and Biotechnology, Universita degli Studi di Milano, Via Adamello 16, 20139 Milan, Italy
Cell 127:509-22. 2006
..Our results indicate that Ubc9- and Mms21-mediated sumoylation functions as a regulatory mechanism, different from that of replication checkpoints, to prevent pathological accumulation of cruciform structures at damaged forks...
- 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
- Synaptonemal complex assembly in C. elegans is dispensable for loading strand-exchange proteins but critical for proper completion of recombination
MONICA P COLAIACOVO
Department of Developmental Biology, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Dev Cell 5:463-74. 2003
..Our data also suggest that early prophase barriers to utilization of sister chromatids as repair templates do not depend on central region assembly...
- The RAD51 gene family, genetic instability and cancer
Medical Research Council, Radiation and Genome Stability Unit, Harwell, Oxfordshire OX11 0RD, UK
Cancer Lett 219:125-35. 2005
- 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...
- Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Nature 453:489-4. 2008
..The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling...
- Generating crossovers by resolution of nicked Holliday junctions: a role for Mus81-Eme1 in meiosis
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
Mol Cell 12:761-74. 2003
..These data demonstrate how crossovers could arise without forming or resolving dHJs using an enzyme that is widely conserved amongst eukaryotes...
- 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...
- Chimeric nucleases stimulate gene targeting in human cells
Matthew H Porteus
Department of Biology, California Institute of Technology, Pasadena CA 91125, USA
Science 300:763. 2003
- Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W Tyson
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
Nature 428:37-43. 2004
..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
- How clonal is Staphylococcus aureus?
Edward J Feil
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
J Bacteriol 185:3307-16. 2003
- 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...
- Mechanism and control of meiotic recombination initiation
Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, and Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, USA
Curr Top Dev Biol 52:1-53. 2001
- Insights into DNA recombination from the structure of a RAD51-BRCA2 complex
University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1GA, UK
Nature 420:287-93. 2002
..Cancer-associated mutations that affect the BRC repeat disrupt its predicted interaction with RAD51, yielding structural insight into mechanisms for cancer susceptibility...
- Two-step red-mediated recombination for versatile high-efficiency markerless DNA manipulation in Escherichia coli
B Karsten Tischer
Cornell University, Ithaca, NY, USA
Biotechniques 40:191-7. 2006
- EXO1-A multi-tasking eukaryotic nuclease
Phuoc T Tran
Graduate Medical Education, St Mary s Medical Center, San Francisco, CA 94117, USA
DNA Repair (Amst) 3:1549-59. 2004
..Here, we review studies in several experimental systems that shed light on the role of Exo1 in these DNA transaction pathways, particularly those that may relate to oncogenesis...
- 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...
- 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...
- 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...
- 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
- 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
- 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
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
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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...
- 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...
- 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...