Control of DNA replication timing in the 3D genome

DNA Replication Timing Enters the Single-Cell Era

(2019) Ichiro Hiratani et al.   Genes

Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains

(2019) Phoebe Oldach et al.   Genes

Genome-wide stability of the DNA replication program in single mammalian cells

(2019) Saori Takahashi et al.   NATURE GENETICS

Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

(2019) Charles A. Seller et al.   GENES & DEVELOPMENT

Replication Timing Becomes Intertwined with 3D Genome Organization

(2019) Jian Ma et al.   CELL

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

(2019) Vishnu Dileep et al.   Stem Cell Reports

A mechanism for epigenetic control of DNA replication

(2018) Courtney G. Sansam et al.   GENES & DEVELOPMENT

Allele-specific control of replication timing and genome organization during development

(2018) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains

(2018) Wanqing Xiang et al.   JOURNAL OF CELL BIOLOGY

The mechanism of eukaryotic CMG helicase activation

(2018) Max E. Douglas et al.   NATURE

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

(2018) Claire Marchal et al.   Nature Protocols

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

The evolution of the temporal program of genome replication

(2018) Nicolas Agier et al.   Nature Communications

Single-cell replication profiling to measure stochastic variation in mammalian replication timing

(2018) Vishnu Dileep et al.   Nature Communications

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Rif1 prolongs the embryonic S phase at the Drosophila mid-blastula transition

(2018) Charles A. Seller et al.   PLOS BIOLOGY

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data

(2018) Yang Yang et al.   Cell Systems

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

Transcription-dependent regulation of replication dynamics modulates genome stability

(2018) Marion Blin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia

(2017) Takayo Sasaki et al.   EXPERIMENTAL HEMATOLOGY

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing

(2017) Dingqiang Fang et al.   GENES & DEVELOPMENT

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

(2017) Joseph C. Siefert et al.   GENOME RESEARCH

H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2

(2017) Carol C.L. Chen et al.   GENOME RESEARCH

L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing

(2017) Emily J. Platt et al.   JOURNAL OF CELL BIOLOGY

DNA replication timing influences gene expression level

(2017) Carolin A. Müller et al.   JOURNAL OF CELL BIOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Programming asynchronous replication in stem cells

(2017) Hagit Masika et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability

(2017) Koichi Utani et al.   NUCLEIC ACIDS RESEARCH

DNA replication timing alterations identify common markers between distinct progeroid diseases

(2017) Juan Carlos Rivera-Mulia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes inS. cerevisiae

(2017) A. Zachary Ostrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programming asynchronous replication in stem cells

(2017) Hagit Masika et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mouse Rif1 is a regulatory subunit of protein phosphatase 1 (PP1)

(2017) Rasa Sukackaite et al.   Scientific Reports

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

(2016) Korey A. Wilson et al.   CELL CYCLE

Replication timing and transcriptional control: beyond cause and effect — part III

(2016) Juan Carlos Rivera-Mulia et al.   CURRENT OPINION IN CELL BIOLOGY

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

(2016) Rossana Foti et al.   MOLECULAR CELL

Replicating Large Genomes: Divide and Conquer

(2016) Juan Carlos Rivera-Mulia et al.   MOLECULAR CELL

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers

(2016) Benoit Miotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression homeostasis during DNA replication

(2016) Y. Voichek et al.   SCIENCE

Influence ofATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells

(2016) Junjie Lu et al.   STEM CELLS AND DEVELOPMENT

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans

(2016) Ehsan Pourkarimi et al.   eLife

Two distinct modes for propagation of histone PTMs across the cell cycle

(2015) Constance Alabert et al.   GENES & DEVELOPMENT

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

(2015) Vishnu Dileep et al.   GENOME RESEARCH

The chromatin environment shapes DNA replication origin organization and defines origin classes

(2015) Christelle Cayrou et al.   GENOME RESEARCH

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

(2015) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

Interaction of Chk1 with Treslin Negatively Regulates the Initiation of Chromosomal DNA Replication

(2015) Cai Guo et al.   MOLECULAR CELL

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Differential DNA mismatch repair underlies mutation rate variation across the human genome

(2015) Fran Supek et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Allele-specific analysis of DNA replication origins in mammalian cells

(2015) Boris Bartholdy et al.   Nature Communications

Drosophila Rif1 is an essential gene and controls late developmental events by direct interaction with PP1-87B

(2015) Easwaran Sreesankar et al.   Scientific Reports

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions

(2015) Marat D. Kazanov et al.   Cell Reports

ASAR15, A cis-Acting Locus that Controls Chromosome-Wide Replication Timing and Stability of Human Chromosome 15

(2015) Nathan Donley et al.   PLoS Genetics

Genetic Variation in Human DNA Replication Timing

(2014) Amnon Koren et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Complex correlations: replication timing and mutational landscapes during cancer and genome evolution

(2014) Jiao Sima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex

(2014) S.-i. Hiraga et al.   GENES & DEVELOPMENT

The Histone Deacetylases Sir2 and Rpd3 Act on Ribosomal DNA to Control the Replication Program in Budding Yeast

(2014) Kazumasa Yoshida et al.   MOLECULAR CELL

A chromatin structure-based model accurately predicts DNA replication timing in human cells

(2014) Y. Gindin et al.   Molecular Systems Biology

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

(2014) Pierre Therizols et al.   SCIENCE

The Distribution of Genomic Variations in Human iPSCs Is Related to Replication-Timing Reorganization during Reprogramming

(2014) Junjie Lu et al.   Cell Reports

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

(2014) Rituparna Mukhopadhyay et al.   PLoS Genetics

The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells

(2014) Franck Picard et al.   PLoS Genetics

Functional redundancy in the nuclear compartmentalization of the late-replicating genome

(2014) Tobias Ragoczy et al.   Nucleus

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins

(2013) Larry D. Mesner et al.   GENOME RESEARCH

The Replication Domain Model: Regulating Replicon Firing in the Context of Large-Scale Chromosome Architecture

(2013) Benjamin D. Pope et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetochores Coordinate Pericentromeric Cohesion and Early DNA Replication by Cdc7-Dbf4 Kinase Recruitment

(2013) Toyoaki Natsume et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Human SIRT1 regulates DNA binding and stability of the Mcm10 DNA replication factor via deacetylation

(2013) Samuel T. Fatoba et al.   NUCLEIC ACIDS RESEARCH

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Replication Timing

(2013) N. Rhind et al.   Cold Spring Harbor Perspectives in Biology

Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains

(2013) Shin-ichiro Takebayashi et al.   Epigenetics & Chromatin

Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

(2013) Nathan Donley et al.   PLoS Genetics

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

Forkhead Transcription Factors Establish Origin Timing and Long-Range Clustering in S. cerevisiae

(2012) Simon R.V. Knott et al.   CELL

Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells

(2012) Daniela Cornacchia et al.   EMBO JOURNAL

Rif1 regulates the replication timing domains on the human genome

(2012) Satoshi Yamazaki et al.   EMBO JOURNAL

Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast

(2012) A. Tazumi et al.   GENES & DEVELOPMENT

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

(2012) G. I. Dellino et al.   GENOME RESEARCH

Conservation of replication timing reveals global and local regulation of replication origin activity

(2012) C. A. Muller et al.   GENOME RESEARCH

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

(2012) T. Ryba et al.   GENOME RESEARCH

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse

(2012) Benjamin D. Pope et al.   HUMAN MOLECULAR GENETICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

3D chromatin conformation correlates with replication timing and is conserved in resting cells

(2012) Benoit Moindrot et al.   NUCLEIC ACIDS RESEARCH

Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization

(2012) Shlomit Farkash-Amar et al.   PLoS One

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

(2012) S.-i. Takebayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

USF Binding Sequences from the HS4 Insulator Element Impose Early Replication Timing on a Vertebrate Replicator

(2012) Vahideh Hassan-Zadeh et al.   PLOS BIOLOGY

Regulation of DNA Replication within the Immunoglobulin Heavy-Chain Locus During B Cell Commitment

(2012) Agnieszka Demczuk et al.   PLOS BIOLOGY

Genome-wide identification and characterization of replication origins by deep sequencing

(2012) Jia Xu et al.   GENOME BIOLOGY

Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding

(2012) Shin-ichiro Takebayashi et al.   Nucleus

Chromatin states in pluripotent, differentiated, and reprogrammed cells

(2011) Cynthia L Fisher et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast

(2011) Davide Mantiero et al.   EMBO JOURNAL

An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression

(2011) Eric P. Stoffregen et al.   HUMAN MOLECULAR GENETICS

Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin

(2011) Corella S. Casas-Delucchi et al.   NUCLEIC ACIDS RESEARCH

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

(2011) Tyrone Ryba et al.   PLoS Computational Biology

Treslin Collaborates with TopBP1 in Triggering the Initiation of DNA Replication

(2010) Akiko Kumagai et al.   CELL

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

(2010) T. Ryba et al.   GENOME RESEARCH

G2 phase chromatin lacks determinants of replication timing

(2010) Junjie Lu et al.   JOURNAL OF CELL BIOLOGY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

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

(2010) Eitan Yaffe 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

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

Genome-wide analysis of the replication program in mammals

(2009) Shlomit Farkash-Amar et al.   CHROMOSOME RESEARCH

Replication timing and transcriptional control: beyond cause and effect—part II

(2009) Ichiro Hiratani et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Allelic inactivation of rDNA loci

(2009) S. Schlesinger et al.   GENES & DEVELOPMENT

Predictable dynamic program of timing of DNA replication in human cells

(2009) R. Desprat et al.   GENOME RESEARCH

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

(2009) I. Hiratani et al.   GENOME RESEARCH

Shifts in Replication Timing Actively Affect Histone Acetylation during Nucleosome Reassembly

(2009) Laura Lande-Diner 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

Assembly of the Cdc45-Mcm2-7-GINS complex in human cells requires the Ctf4/And-1, RecQL4, and Mcm10 proteins

(2009) J.-S. Im et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G9a selectively represses a class of late-replicating genes at the nuclear periphery

(2009) T. Yokochi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

DNA replication timing of the human  -globin domain is controlled by histone modification at the origin

(2008) A. Goren et al.   GENES & DEVELOPMENT

Global organization of replication time zones of the mouse genome

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

Genome-wide studies highlight indirect links between human replication origins and gene regulation

(2008) J.-C. Cadoret 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