DNA in Science

1.DNA from Pre-Clovis Human Coprolites in Oregon, North America
M. Thomas P. Gilbert,1* Dennis L. Jenkins,2* Anders Götherstrom,3 Nuria Naveran,4 Juan J. Sanchez,5 Michael Hofreiter,6 Philip Francis Thomsen,1 Jonas Binladen,1 Thomas F. G. Higham,7 Robert M. Yohe, II,8 Robert Parr,8 Linda Scott Cummings,9 Eske Willerslev1
The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America at about 11,000 to 10,800 radiocarbon years before the present (14C years B.P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, in south-central Oregon, by 12,300 14C years B.P., through the recovery of human mitochondrial DNA (mtDNA) from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 14C years earlier than currently accepted dates for the Clovis complex.
1 Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.2 Museum of Natural and Cultural History, 1224 University of Oregon, Eugene, OR 97403-1224, USA.3 Department of Evolutionary Biology, Uppsala University, Norbyvagten 18D, 74236 Uppsala, Sweden.4 Instituto de Medicina Legal, Facultad de Medicina, University of Santiago de Compostela, San Francisco s/n 15782, Santiago de Compostela, Spain.5 National Institute of Toxicology and Forensic Science, Canary Islands Delegation, 38320 Tenerife, Spain.6 Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.7 Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK.8 Department of Sociology/Anthropology, California State University, 9001 Stockdale Highway, Bakersfield, CA 93311, USA.9 Palaeo Research Institute, 2675 Youngfield Street, Golden, CO 80401, USA.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: ewillerslev@bi.ku.dk
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2.ROS-Generating Mitochondrial DNA Mutations Can Regulate Tumor Cell Metastasis
Kaori Ishikawa,1,2,3* Keizo Takenaga,4,5* Miho Akimoto,5 Nobuko Koshikawa,4 Aya Yamaguchi,1 Hirotake Imanishi,1 Kazuto Nakada,1,2 Yoshio Honma,5 Jun-Ichi Hayashi1
Mutations in mitochondrial DNA (mtDNA) occur at high frequency in human tumors, but whether these mutations alter tumor cell behavior has been unclear. We used cytoplasmic hybrid (cybrid) technology to replace the endogenous mtDNA in a mouse tumor cell line that was poorly metastatic with mtDNA from a cell line that was highly metastatic, and vice versa. Using assays of metastasis in mice, we found that the recipient tumor cells acquired the metastatic potential of the transferred mtDNA. The mtDNA conferring high metastatic potential contained G13997A and 13885insC mutations in the gene encoding NADH (reduced form of nicotinamide adenine dinucleotide) dehydrogenase subunit 6 (ND6). These mutations produced a deficiency in respiratory complex I activity and were associated with overproduction of reactive oxygen species (ROS). Pretreatment of the highly metastatic tumor cells with ROS scavengers suppressed their metastatic potential in mice. These results indicate that mtDNA mutations can contribute to tumor progression by enhancing the metastatic potential of tumor cells.
1 Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.2 Tsukuba Advanced Research Alliance Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.3 Japan Society for the Promotion of Science (JSPS), 8 Ichibancho, Chiyoda-ku, Tokyo 102-8472, Japan.4 Division of Chemotherapy, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan.5 Shimane University Faculty of Medicine, 89-1 Enya-cho, Izumo, Shimane 693-8501, Japan.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: jih45@sakura.cc.tsukuba.ac.jp
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3.Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions
Jean-Pierre Vartanian, Denise Guétard, Michel Henry, Simon Wain-Hobson*
Cytidine deaminases of the APOBEC3 family all have specificity for single-stranded DNA, which may become exposed during replication or transcription of double-stranded DNA. Three human APOBEC3A (hA3A), hA3B, and hA3H genes are expressed in keratinocytes and skin, leading us to determine whether genetic editing of human papillomavirus (HPV) DNA occurred. In a study of HPV1a plantar warts and HPV16 precancerous cervical biopsies, hyperedited HPV1a and HPV16 genomes were found. Strictly analogous results were obtained from transfection experiments with HPV plasmid DNA and the three nuclear localized enzymes: hA3A, hA3C, and hA3H. Thus, stochastic or transient overexpression of APOBEC3 genes may expose the genome to a broad spectrum of mutations that could influence the development of tumors.
Molecular Retrovirology Unit, Institut Pasteur, 28 Rue de Docteur Roux, 75724 Paris cedex 15, France.
* To whom correspondence should be addressed. E-mail: simon@pasteur.fr
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4.DNA From Fossil Feces Breaks Clovis Barrier
Michael Balter
An international team reports online in Science this week what some experts consider the strongest evidence yet for an earlier peopling of the Americas: 14,000-year-old ancient DNA from fossilized human excrement (coprolites), found in caves in south-central Oregon.
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5.Single-Molecule DNA Sequencing of a Viral Genome
Timothy D. Harris,1* Phillip R. Buzby,1 Hazen Babcock,1 Eric Beer,1 Jayson Bowers,1 Ido Braslavsky,2 Marie Causey,1 Jennifer Colonell,1 James DiMeo,1 J. William Efcavitch,1 Eldar Giladi,1 Jaime Gill,1 John Healy,1 Mirna Jarosz,1 Dan Lapen,1 Keith Moulton,1 Stephen R. Quake,3 Kathleen Steinmann,1 Edward Thayer,1 Anastasia Tyurina,1 Rebecca Ward,1 Howard Weiss,1 Zheng Xie1
The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.
1 Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, USA.2 Department of Physics and Astronomy, Ohio University, Athens, OH 45701, USA.3 Department of Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA.
* To whom correspondence should be addressed. E-mail: tharris@helicosbio.com
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6.Nutritional Control of Reproductive Status in Honeybees via DNA Methylation
R. Kucharski,* J. Maleszka,* S. Foret, R. Maleszka
Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly–like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA–treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status.
Molecular Genetics and Evolution, ARC Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra ACT 0200, Australia.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: maleszka@rsbs.anu.edu.au
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7.Proposal to 'Wikify' GenBank Meets Stiff Resistance
Elizabeth Pennisi
In a letter in this week's issue of Science, a group of mycologists urges GenBank to allow researchers who discover inaccuracies in the database to append corrections. GenBank, however, says such a fix would cause more problems than it solves.
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8.An Oncogene-Induced DNA Damage Model for Cancer Development
Thanos D. Halazonetis,1* Vassilis G. Gorgoulis,2 Jiri Bartek3
Of all types of DNA damage, DNA double-strand breaks (DSBs) pose the greatest challenge to cells. One might have, therefore, anticipated that a sizable number of DNA DSBs would be incompatible with cell proliferation. Yet recent experimental findings suggest that, in both precancerous lesions and cancers, activated oncogenes induce stalling and collapse of DNA replication forks, which in turn leads to formation of DNA DSBs. This continuous formation of DNA DSBs may contribute to the genomic instability that characterizes the vast majority of human cancers. In addition, in precancerous lesions, these DNA DSBs activate p53, which, by inducing apoptosis or senescence, raises a barrier to tumor progression. Breach of this barrier by various mechanisms, most notably by p53 mutations, that impair the DNA damage response pathway allows cancers to develop. Thus, oncogene-induced DNA damage may explain two key features of cancer: genomic instability and the high frequency of p53 mutations.
1 Department of Molecular Biology and Department of Biochemistry, University of Geneva, CH-1205 Geneva, Switzerland.2 Department of Histology and Embryology, School of Medicine, University of Athens, GR-11527 Athens, Greece.3 Institute of Cancer Biology and Centre for Genotoxic Stress Research, Danish Cancer Society, DK-2100 Copenhagen, Denmark.
* To whom correspondence should be addressed. E-mail: Thanos.Halazonetis@molbio.unige.ch
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9.DNA Assembles Materials From the Ground Up
Robert F. Service
On page 594 of this week's issue of Science, researchers report using DNA as tweezers to pick up compounds and place them where they're wanted. The technique could help researchers put chains of molecules together to answer questions such as how different enzymes work together in a series.
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10.DNA SEQUENCING:A Plan to Capture Human Diversity in 1000 Genomes
Jocelyn Kaiser
Over the next 3 years, an international team plans to create a massive new catalog containing the complete genome sequences of 1000 individuals. It will help fill out the list of new genetic markers for common diseases that came out in 2007.
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11.Control of Genic DNA Methylation by a jmjC Domain-Containing Protein in Arabidopsis thaliana
Hidetoshi Saze,* Akiko Shiraishi, Asuka Miura, Tetsuji Kakutani
Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.
Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
* To whom correspondence should be addressed. E-mail: hsaze@lab.nig.ac.jp
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12.DNA Oxidation as Triggered by H3K9me2 Demethylation Drives Estrogen-Induced Gene Expression
Bruno Perillo,1* Maria Neve Ombra,1* Alessandra Bertoni,2 Concetta Cuozzo,3 Silvana Sacchetti,3 Annarita Sasso,2 Lorenzo Chiariotti,2 Antonio Malorni,1 Ciro Abbondanza,4 Enrico V. Avvedimento2
Modifications at the N-terminal tails of nucleosomal histones are required for efficient transcription in vivo. We analyzed how H3 histone methylation and demethylation control expression of estrogen-responsive genes and show that a DNA-bound estrogen receptor directs transcription by participating in bending chromatin to contact the RNA polymerase II recruited to the promoter. This process is driven by receptor-targeted demethylation of H3 lysine 9 at both enhancer and promoter sites and is achieved by activation of resident LSD1 demethylase. Localized demethylation produces hydrogen peroxide, which modifies the surrounding DNA and recruits 8-oxoguanine–DNA glycosylase 1 and topoisomeraseIIβ, triggering chromatin and DNA conformational changes that are essential for estrogen-induced transcription. Our data show a strategy that uses controlled DNA damage and repair to guide productive transcription.
1 Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche (C.N.R.), 83100 Avellino, Italy.2 Dipartimento di Biologia e Patologia Cellulare e Molecolare "L. Califano," Università degli Studi "Federico II," 80131 Naples, Italy.3 Naples Oncogenomic Center, Centro di Ingegneria Genetica (CEINGE), Biotecnologie Avanzate, 80131 Naples, Italy.4 Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, 80138 Naples, Italy.
* These authors contributed equally to this paper.
To whom correspondence should be addressed. E-mail: perillo@unina.it (B.P.); avvedim@unina.it (E.V.A.)
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13.Orchestration of the DNA-Damage Response by the RNF8 Ubiquitin Ligase
Nadine K. Kolas,1* J. Ross Chapman,2* Shinichiro Nakada,1* Jarkko Ylanko,1,3 Richard Chahwan,2 Frédéric D. Sweeney,1,3 Stephanie Panier,1 Megan Mendez,1 Jan Wildenhain,1 Timothy M. Thomson,4 Laurence Pelletier,1,3 Stephen P. Jackson,2 Daniel Durocher1,3
Cells respond to DNA double-strand breaks by recruiting factors such as the DNA-damage mediator protein MDC1, the p53-binding protein 1 (53BP1), and the breast cancer susceptibility protein BRCA1 to sites of damaged DNA. Here, we reveal that the ubiquitin ligase RNF8 mediates ubiquitin conjugation and 53BP1 and BRCA1 focal accumulation at sites of DNA lesions. Moreover, we establish that MDC1 recruits RNF8 through phosphodependent interactions between the RNF8 forkhead-associated domain and motifs in MDC1 that are phosphorylated by the DNA-damage activated protein kinase ataxia telangiectasia mutated (ATM). We also show that depletion of the E2 enzyme UBC13 impairs 53BP1 recruitment to sites of damage, which suggests that it cooperates with RNF8. Finally, we reveal that RNF8 promotes the G2/M DNA damage checkpoint and resistance to ionizing radiation. These results demonstrate how the DNA-damage response is orchestrated by ATM-dependent phosphorylation of MDC1 and RNF8-mediated ubiquitination.
1 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G1X5, Ontario, Canada.2 The Wellcome Trust and Cancer Research UK Gurdon Institute, and the Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.3 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.4 Department of Molecular and Cellular Biology, Instituto de Biología Molecular de Barcelona calle Jordi Girona 18-26, 08034 Barcelona, Spain.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: durocher@mshri.on.ca (D.D.); s.jackson@gurdon.cam.ac.uk (S.P.J.)
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14.End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes
Michi Nakata,1* Giuliano Zanchetta,2* Brandon D. Chapman,3 Christopher D. Jones,1 Julie O. Cross,4 Ronald Pindak,3 Tommaso Bellini,2 Noel A. Clark1
Short complementary B-form DNA oligomers, 6 to 20 base pairs in length, are found to exhibit nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal ordering. Structural study shows that these phases are produced by the end-to-end adhesion and consequent stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. Upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the DNA present is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers.
1 Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, CO 80309–0390, USA.2 Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università di Milano, Milano, Italy.3 National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA.4 Advanced Photon Source, Argonne National Laboratory, Argonne, IL60439, USA.
* These authors contributed equally to this work.
Deceased.
To whom correspondence should be addressed. E-mail: tommaso.bellini@unimi.it (T.B.); noel.clark@colorado.edu (N.A.C.)
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15.DNA Circuits Get Up to Speed
Roy Bar-Ziv
An amplification mechanism brings DNA circuits closer to practical applications.
The author is in the Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel. E-mail: roy.bar-ziv@weizmann.ac.il
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16.A key aspect of electronic circuits is amplification or gain, so that low signals can be distinguished from any persistent background.
Zhang et al. (p. 1121; see the Perspective by Bar-Ziv) show how gain can be achieved in biochemical circuits. They have designed complex catalytic networks based on DNA in which the output oligonucleotides that are released go on to act as catalysts for other reactions. The process is designed to be entropy driven so that the pathways for reactions are well controlled and can be modified at will. Possible applications lie in the field of catalysis, sensor development, the development of enzyme-free alternative for the polymerase chain reaction, and the construction of nanomachines.
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17.Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA
David Yu Zhang,1 Andrew J. Turberfield,2 Bernard Yurke,3* Erik Winfree1
Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.
1 Computation and Neural Systems, California Institute of Technology, MC 136-93, 1200 East California Boulevard, Pasadena, CA91125, USA.2 Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK.3 Bell Laboratories, Alcatel-Lucent, Murray Hill, NJ 07974, USA.
* Present address: Materials Science and Engineering Department, Boise State University, Boise, ID 83725, USA.
To whom correspondence should be addressed. E-mail: winfree@caltech.edu (E.W.); dzhang@dna.caltech.edu (D.Y.Z.)
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18.Bypass of DNA Lesions Generated During Anticancer Treatment with Cisplatin by DNA Polymerase
Aaron Alt,1* Katja Lammens,1,2* Claudia Chiocchini,1 Alfred Lammens,1,2 J. Carsten Pieck,1 David Kuch,1 Karl-Peter Hopfner,1,2 Thomas Carell1
DNA polymerase (Pol ) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis–syn thymine dimers. We present structural and biochemical analysis of how Pol copies Pt-GG–containing DNA. The damaged DNA is bound in an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an active conformation, driven by hydrogen bonding of the templating base to the dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick base pair to dCTP and is biochemically efficient and accurate. In contrast, bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and dATP as a result of the presence of the rigid Pt cross-link. Our analysis reveals the set of structural features that enable Pol to replicate across strongly distorting DNA lesions.
1 Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilians University, D-81377 Munich, Germany.2 Gene Center at the Department of Chemistry and Biochemistry, Ludwig Maximilians University, D-81377 Munich, Germany.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: hopfner@lmb.uni-muenchen.de (K.-P.H.); thomas.carell@cup.uni-muenchen.de (T.C.)
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19.Ancient DNA Reveals Neandertals With Red Hair, Fair Complexions
Elizabeth Culotta
A pigmentation gene from the bones of two Neandertals, reported online this week in Science (www.sciencemag.org/cgi/content/abstract/1147417), indicates that at least some Neandertals had pale skin and red hair, similar to some of the Homo sapiens who today inhabit their European homeland.
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20.Mitochondrial DNA as a Genomic Jigsaw Puzzle
William Marande and Gertraud Burger*
In mitochondria of the unicellular eukaryote Diplonema, genes are systematically fragmented into small pieces that are encoded on separate chromosomes, transcribed individually, and then concatenated into contiguous messenger RNA molecules
Department of Biochemistry, Université de Montréal, Montréal, Quebec H3T 1J4, Canada.
* To whom correspondence should be addressed. E-mail: Gertraud.Burger@UMontreal.ca
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21.Structure of a NHEJ Polymerase-Mediated DNA Synaptic Complex
Nigel C. Brissett,1* Robert S. Pitcher,1* Raquel Juarez,2 Angel J. Picher,2 Andrew J. Green,1 Timothy R. Dafforn,3 Gavin C. Fox,4 Luis Blanco,2 Aidan J. Doherty1
Nonhomologous end joining (NHEJ) is a critical DNA double-strand break (DSB) repair pathway required to maintain genome stability. Many prokaryotes possess a minimalist NHEJ apparatus required to repair DSBs during stationary phase, composed of two conserved core proteins, Ku and ligase D (LigD). The crystal structure of Mycobacterium tuberculosis polymerase domain of LigD mediating the synapsis of two noncomplementary DNA ends revealed a variety of interactions, including microhomology base pairing, mismatched and flipped-out bases, and 3' termini forming hairpin-like ends. Biochemical and biophysical studies confirmed that polymerase-induced end synapsis also occurs in solution. We propose that this DNA synaptic structure reflects an intermediate bridging stage of the NHEJ process, before end processing and ligation, with both the polymerase and the DNA sequence playing pivotal roles in determining the sequential order of synapsis and remodeling before end joining.
1 Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.2 Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain.3 Department of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.4 European Synchrotron Radiation Facility, LLS-BM16, Grenoble Cedex 9, France.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: lblanco@cbm.uam.es (L.B.); ajd21@sussex.ac.uk (A.J.D.)
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22.UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells
Magnolia Bostick,1* Jong Kyong Kim,2* Pierre-Olivier Estève,2 Amander Clark,1 Sriharsa Pradhan,2 Steven E. Jacobsen1,3
Epigenetic inheritance in mammals relies in part on robust propagation of DNA methylation patterns throughout development. We show that the protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1), also known as NP95 in mouse and ICBP90 in human, is required for maintaining DNA methylation. UHRF1 colocalizes with the maintenance DNA methyltransferase protein DNMT1 throughout S phase. UHRF1 appears to tether DNMT1 to chromatin through its direct interaction with DNMT1. Furthermore UHRF1 contains a methyl DNA binding domain, the SRA (SET and RING associated) domain, that shows strong preferential binding to hemimethylated CG sites, the physiological substrate for DNMT1. These data suggest that UHRF1 may help recruit DNMT1 to hemimethylated DNA to facilitate faithful maintenance of DNA methylation.
1 Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.2 New England BioLabs, Ipswich, MA 01938, USA.3 Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: pradhan@neb.com (S.P.); jacobsen@ucla.edu (S.E.J.)
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