Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

(2017) Marta Rodríguez-Martínez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

(2017) Marta Rodríguez-Martínez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Accessing the Inaccessible: The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants

(2015) Wei Feng et al.   Annual Review of Genetics

Linking replication stress with heterochromatin formation

(2015) Ivaylo Nikolov et al.   CHROMOSOMA

Transposable elements and G-quadruplexes

(2015) Eduard Kejnovsky et al.   CHROMOSOME RESEARCH

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2015) Christelle Cayrou et al.   GENOME RESEARCH

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

Links between genome replication and chromatin landscapes

(2015) Joana Sequeira-Mendes et al.   PLANT JOURNAL

Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants

(2015) Tao Zhang et al.   PLANT PHYSIOLOGY

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

(2015) Federico Comoglio et al.   Cell Reports

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

(2014) A.-L. Valton et al.   EMBO JOURNAL

DNA replication and transcription programs respond to the same chromatin cues

(2014) Y. Lubelsky et al.   GENOME RESEARCH

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

Temporal and spatial regulation of eukaryotic DNA replication: From regulated initiation to genome-scale timing program

(2014) Claire Renard-Guillet et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Genetic and epigenetic determinants of DNA replication origins, position and activation

(2013) Marcel Méchali et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Characterization of the Early Events Leading to Totipotency in an Arabidopsis Protoplast Liquid Culture by Temporal Transcript Profiling

(2013) M.-C. Chupeau et al.   PLANT CELL

New insights into replication origin characteristics in metazoans

(2012) Christelle Cayrou et al.   CELL CYCLE

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome-scale identification of active DNA replication origins

(2012) Christelle Cayrou et al.   METHODS

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

Retention of triplicated phytoene synthase (PSY) genes in Brassica napus L. and its diploid progenitors during the evolution of the Brassiceae

(2012) Pablo D. Cárdenas et al.   THEORETICAL AND APPLIED GENETICS

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks

(2011) Celina Costas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

(2010) Yannick Jacob et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

(2009) Joana Sequeira-Mendes et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY