GENETIC VARIATION AND DNA REPLICATION TIMING, OR WHY IS THERE LATE REPLICATING DNA?

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

(2011) Irene Chiolo et al.   CELL

Chk1 is activated at the midblastula transition inXenopus laevisembryos independently of DNA content and the cyclin E/Cdk2 developmental timer

(2011) Nassiba Adjerid et al.   CELL CYCLE

DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells

(2011) Zhiyong Mao et al.   CELL CYCLE

Temporal differences in DNA replication during the S phase using single fiber analysis of normal human fibroblasts and glioblastoma T98G cells

(2011) Rebecca A. Frum et al.   CELL CYCLE

Factors determining DNA double-strand break repair pathway choice in G2 phase

(2011) Atsushi Shibata et al.   EMBO JOURNAL

The effect of the intra-S-phase checkpoint on origins of replication in human cells

(2011) Neerja Karnani et al.   GENES & DEVELOPMENT

Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing

(2011) Gregory I. Lang et al.   Genome Biology and Evolution

USP1 deubiquitinase maintains phosphorylated CHK1 by limiting its DDB1-dependent degradation

(2011) Jean-Hugues Guervilly et al.   HUMAN MOLECULAR GENETICS

Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site

(2011) Anne Letessier et al.   NATURE

The histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1

(2011) Chung-Yi Liang et al.   NUCLEIC ACIDS RESEARCH

The dynamic replicon: adapting to a changing cellular environment

(2010) John Herrick   BIOESSAYS

Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages

(2010) Lesley T Lancaster   BMC EVOLUTIONARY BIOLOGY

The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution

(2010) Rodney D Adam et al.   BMC GENOMICS

Beyond heterochromatin: SIR2 inhibits the initiation of DNA replication

(2010) Catherine A. Fox et al.   CELL CYCLE

S-phase progression in mammalian cells: modelling the influence of nuclear organization

(2010) Alex Shaw et al.   CHROMOSOME RESEARCH

Developmental Control of Late Replication and S Phase Length

(2010) Antony W. Shermoen et al.   CURRENT BIOLOGY

Maternal control of early mouse development

(2010) L. Li et al.   DEVELOPMENT

The influence of heterochromatin on DNA double strand break repair: Getting the strong, silent type to relax

(2010) Aaron A. Goodarzi et al.   DNA REPAIR

Genome Size and Species Diversification

(2010) Ken Kraaijeveld   Evolutionary Biology

Jumping genes and epigenetics: Towards new species

(2010) Rita Rebollo et al.   GENE

Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

(2010) C. F. Mugal et al.   Genome Biology and Evolution

Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus

(2010) Kenneth M. Flynn et al.   Genome Biology and Evolution

Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes

(2010) C. L. Chen et al.   GENOME RESEARCH

MRC1-dependent scaling of the budding yeast DNA replication timing program

(2010) A. Koren et al.   GENOME RESEARCH

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

The mutational spectrum of non-CpG DNA varies with CpG content

(2010) J.-C. Walser et al.   GENOME RESEARCH

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

(2010) N Zamudio et al.   HEREDITY

Rapid and transient recruitment of DNMT1 to DNA double-strand breaks is mediated by its interaction with multiple components of the DNA damage response machinery

(2010) Kyungsoo Ha et al.   HUMAN MOLECULAR GENETICS

ATR/Chk1 pathway is essential for resumption of DNA synthesis and cell survival in UV-irradiated XP variant cells

(2010) Emmanuelle Despras et al.   HUMAN MOLECULAR GENETICS

Akt/PKB suppresses DNA damage processing and checkpoint activation in late G2

(2010) Naihan Xu et al.   JOURNAL OF CELL BIOLOGY

Role of ATM and the Damage Response Mediator Proteins 53BP1 and MDC1 in the Maintenance of G2/M Checkpoint Arrest

(2010) A. Shibata et al.   MOLECULAR AND CELLULAR BIOLOGY

A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates

(2010) Jessica A. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conserved Antagonism between JMJD2A/KDM4A and HP1γ during Cell Cycle Progression

(2010) Joshua C. Black et al.   MOLECULAR CELL

Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing

(2010) Scott Cheng-Hsin Yang et al.   Molecular Systems Biology

Higher-order chromatin structure in DSB induction, repair and misrepair

(2010) Martin Falk et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Ubiquitin-dependent DNA damage bypass is separable from genome replication

(2010) Yasukazu Daigaku et al.   NATURE

Phosphorylation of MLL by ATR is required for execution of mammalian S-phase checkpoint

(2010) Han Liu et al.   NATURE

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Evaluating genome-scale approaches to eukaryotic DNA replication

(2010) David M. Gilbert   NATURE REVIEWS GENETICS

Dynamic changes in histone acetylation regulate origins of DNA replication

(2010) Ashwin Unnikrishnan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Silenced yeast chromatin is maintained by Sir2 in preference to permitting histone acetylations for efficient NER

(2010) A. Irizar et al.   NUCLEIC ACIDS RESEARCH

Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions

(2010) Rachel Amouroux et al.   NUCLEIC ACIDS RESEARCH

Chk1 promotes replication fork progression by controlling replication initiation

(2010) E. Petermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable element insertions have strongly affected human evolution

(2010) R. J. Britten   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of DNA Replication Control Is a Potent Inducer of Gene Amplification

(2010) B. M. Green et al.   SCIENCE

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

DNA double-strand break repair and the evolution of intron density

(2010) Ashley Farlow et al.   TRENDS IN GENETICS

Evolutionary dynamics of transposable elements in a small RNA world

(2010) Justin P. Blumenstiel   TRENDS IN GENETICS

Chk1 suppressed cell death

(2010) Mark Meuth   Cell Division

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture

(2010) Eitan Yaffe et al.   PLoS Genetics

Replication Timing of Human Telomeres Is Chromosome Arm–Specific, Influenced by Subtelomeric Structures and Connected to Nuclear Localization

(2010) Nausica Arnoult et al.   PLoS Genetics

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State

(2010) Tae-Jin Lee et al.   PLoS Genetics

S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci

(2010) Apolinar Maya-Mendoza et al.   PLoS Genetics

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

Regulators of ribonucleotide reductase inhibit Ty1 mobility in Saccharomyces cerevisiae

(2010) John P O'Donnell et al.   Mobile DNA

The impact of heterochromatin on DSB repair

(2009) Aaron A. Goodarzi et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Why do species vary in their rate of molecular evolution?

(2009) L. Bromham   Biology Letters

Establishing the Program of Origin Firing during S Phase in Fission Yeast

(2009) Pei-Yun Jenny Wu et al.   CELL

Reconciling stochastic origin firing with defined replication timing

(2009) Nicholas Rhind et al.   CHROMOSOME RESEARCH

Domain-wide regulation of DNA replication timing during mammalian development

(2009) Benjamin D. Pope et al.   CHROMOSOME RESEARCH

Temporal regulation of DNA replication in mammalian cells

(2009) Juan Méndez   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The folding and unfolding of eukaryotic chromatin

(2009) Andrew Bassett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

(2009) Andrea Beucher et al.   EMBO JOURNAL

Implication of Checkpoint Kinase-dependent Up-regulation of Ribonucleotide Reductase R2 in DNA Damage Response

(2009) Yong-Wei Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA replication times the cell cycle and contributes to the mid-blastula transition inDrosophilaembryos

(2009) Mark L. McCleland et al.   JOURNAL OF CELL BIOLOGY

Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents

(2009) C. J. Pink et al.   MOLECULAR BIOLOGY AND EVOLUTION

The F Box Protein Fbx6 Regulates Chk1 Stability and Cellular Sensitivity to Replication Stress

(2009) You-Wei Zhang et al.   MOLECULAR CELL

The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus

(2009) Makoto T. Hayashi et al.   NATURE CELL BIOLOGY

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?

(2009) Anita Göndör et al.   NATURE REVIEWS GENETICS

Histone H3 Lys79 methylation is required for efficient nucleotide excision repair in a silenced locus of Saccharomyces cerevisiae

(2009) Shubho Chaudhuri et al.   NUCLEIC ACIDS RESEARCH

Epigenetic responses to environmental change and their evolutionary implications

(2009) B. M. Turner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

H3 K36 Methylation Helps Determine the Timing of Cdc45 Association with Replication Origins

(2009) Fiona Pryde et al.   PLoS One

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

(2009) Arach Goldar et al.   PLoS One

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

(2009) D. R. Denver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cyclin A-Cdk1 regulates the origin firing program in mammalian cells

(2009) Y. Katsuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation as an active force in promoting genetic evolution

(2009) Chris Venditti et al.   TRENDS IN ECOLOGY & EVOLUTION

Heterochromatic Genome Stability Requires Regulators of Histone H3 K9 Methylation

(2009) Jamy C. Peng et al.   PLoS Genetics

A Strong Nucleotypic Effect on the Cell Cycle Regardless of Ploidy Level

(2008) D. Francis et al.   ANNALS OF BOTANY

Essential role of Chk1 in S phase progression through regulation of RNR2 expression

(2008) Hiromichi Naruyama et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

(2008) Aleah K Fox et al.   BMC EVOLUTIONARY BIOLOGY

Broad Overexpression of Ribonucleotide Reductase Genes in Mice Specifically Induces Lung Neoplasms

(2008) X. Xu et al.   CANCER RESEARCH

Apoptosis induced by replication inhibitors in Chk1-depleted cells is dependent upon the helicase cofactor Cdc45

(2008) R Rodriguez et al.   CELL DEATH AND DIFFERENTIATION

Global regulation of genome duplication in eukaryotes: an overview from the epifluorescence microscope

(2008) John Herrick et al.   CHROMOSOMA

Identification of pathways controlling DNA damage induced mutation in Saccharomyces cerevisiae

(2008) Ewa T. Lis et al.   DNA REPAIR

Comparison of nonhomologous end joining and homologous recombination in human cells

(2008) Z MAO et al.   DNA REPAIR

Rtt101 and Mms1 in budding yeast form a CUL4DDB1-like ubiquitin ligase that promotes replication through damaged DNA

(2008) Iram Waris Zaidi et al.   EMBO REPORTS

Molecular Population Genetics of Drosophila Subtelomeric DNA

(2008) Jennifer A. Anderson et al.   GENETICS

The Temporal Program of Chromosome Replication: Genomewide Replication in clb5  Saccharomyces cerevisiae

(2008) H. J. McCune et al.   GENETICS

The Cellular, Developmental and Population-Genetic Determinants of Mutation-Rate Evolution

(2008) M. Lynch   GENETICS

Global organization of replication time zones of the mouse genome

(2008) S. Farkash-Amar et al.   GENOME RESEARCH

Spatial organization of nucleotide excision repair proteins after UV-induced DNA damage in the human cell nucleus

(2008) L. Solimando et al.   JOURNAL OF CELL SCIENCE

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

(2008) G.-F. Richard et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Hsk1(Cdc7) Replication Kinase Regulates Origin Efficiency

(2008) Prasanta K. Patel et al.   MOLECULAR BIOLOGY OF THE CELL

Novel Control of S Phase of the Cell Cycle by Ubiquitin-conjugating Enzyme H7

(2008) Elizabeth A. Whitcomb et al.   MOLECULAR BIOLOGY OF THE CELL

ATM Signaling Facilitates Repair of DNA Double-Strand Breaks Associated with Heterochromatin

(2008) Aaron A. Goodarzi et al.   MOLECULAR CELL

DNA mismatch repair efficiency and fidelity are elevated during DNA synthesis in human cells

(2008) Michael A. Edelbrock et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

A Cdc7 kinase inhibitor restricts initiation of DNA replication and has antitumor activity

(2008) Alessia Montagnoli et al.   Nature Chemical Biology

Regulation of DNA repair throughout the cell cycle

(2008) Dana Branzei et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts

(2008) H. Labit et al.   NUCLEIC ACIDS RESEARCH

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY

Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation

(2008) Navin Elango et al.   PLoS Computational Biology

Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts

(2008) Leonid Teytelman et al.   PLoS Genetics