Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila

Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks

(2018) Kathrin S Heinz et al.   NUCLEIC ACIDS RESEARCH

Chromatin conformation regulates the coordination between DNA replication and transcription

(2018) Ricardo Almeida et al.   Nature Communications

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

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

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

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

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

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Conflict Resolution in the Genome: How Transcription and Replication Make It Work

(2016) Stephan Hamperl et al.   CELL

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

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

Direct interrogation of the role of H3K9 in metazoan heterochromatin function

(2016) Taylor J.R. Penke et al.   GENES & DEVELOPMENT

TALE-light imaging reveals maternally guided, H3K9me2/3-independent emergence of functional heterochromatin inDrosophilaembryos

(2016) Kai Yuan et al.   GENES & DEVELOPMENT

Dosage Compensation in Drosophila--a Model for the Coordinate Regulation of Transcription

(2016) M. I. Kuroda et al.   GENETICS

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

(2016) Rossana Foti 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

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

Interrogating the Function of Metazoan Histones using Engineered Gene Clusters

(2015) Daniel J. McKay et al.   DEVELOPMENTAL CELL

Replication timing is regulated by the number of MCMs loaded at origins

(2015) Shankar P. Das et al.   GENOME RESEARCH

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

Genetic Variation in Human DNA Replication Timing

(2014) Amnon Koren et al.   CELL

DNA replication and transcription programs respond to the same chromatin cues

(2014) Y. Lubelsky et al.   GENOME RESEARCH

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome

(2014) Jared M. Peace et al.   PLoS One

Titration of Four Replication Factors Is Essential for the Xenopus laevis Midblastula Transition

(2013) C. Collart et al.   SCIENCE

DNA replication timing, genome stability and cancer

(2013) Nathan Donley et al.   SEMINARS IN CANCER BIOLOGY

DNA Replication Timing

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

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

(2012) T. Ryba et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Davide Mantiero et al.   EMBO JOURNAL

Analysis of model replication origins in Drosophila reveals new aspects of the chromatin landscape and its relationship to origin activity and the prereplicative complex

(2011) Jun Liu et al.   MOLECULAR BIOLOGY OF THE CELL

Chromodomain-Mediated Oligomerization of HP1 Suggests a Nucleosome-Bridging Mechanism for Heterochromatin Assembly

(2011) Daniele Canzio et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Developmental Control of Late Replication and S Phase Length

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

A genetic system to assess in vivo the functions of histones and histone modifications in higher eukaryotes

(2010) Ufuk Günesdogan et al.   EMBO REPORTS

Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome

(2010) M. Schwaiger et al.   GENOME RESEARCH

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Chromatin signatures of the Drosophila replication program

(2010) M. L. Eaton et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

(2010) Oliver Bell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Expression in Aneuploid Drosophila S2 Cells

(2010) Yu Zhang et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Reconciling stochastic origin firing with defined replication timing

(2009) Nicholas Rhind et al.   CHROMOSOME RESEARCH

Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome

(2009) M. Schwaiger et al.   GENES & DEVELOPMENT

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

(2009) H. K. MacAlpine et al.   GENOME RESEARCH

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation

(2009) Marnie E Gelbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The emerging field of dynamic lysine methylation of non-histone proteins

(2008) Jing Huang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY