Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Polycomb silencing: from linear chromatin domains to 3D chromosome folding

(2014) Thierry Cheutin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

(2014) E. J. Brown et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Citrullination regulates pluripotency and histone H1 binding to chromatin

(2014) Maria A. Christophorou et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Every amino acid matters: essential contributions of histone variants to mammalian development and disease

(2014) Ian Maze 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

Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling

(2014) Mariliis Tark-Dame et al.   PLoS Computational Biology

Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes

(2014) Huan Shu et al.   GENOME BIOLOGY

Large-scale chromatin organization: the good, the surprising, and the still perplexing

(2013) Andrew S Belmont   CURRENT OPINION IN CELL BIOLOGY

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst 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

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

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

(2013) Takashi Nagano et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

(2013) Stefan Grob et al.   GENOME BIOLOGY

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization

(2012) Pedro Crevillén et al.   EMBO JOURNAL

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

(2012) H. Stroud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

(2012) G. Moissiard et al.   SCIENCE

Distinct modes of DNA accessibility in plant chromatin

(2012) Huan Shu et al.   Nature Communications

Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome

(2012) Heike Wollmann et al.   PLoS Genetics

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Epigenetic modifications in plants: an evolutionary perspective

(2011) Suhua Feng et al.   CURRENT OPINION IN PLANT BIOLOGY

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model

(2010) Jessica L Larson et al.   BMC BIOINFORMATICS

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

(2010) Guillaume J. Filion 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

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

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

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression

(2010) Junli Zhou et al.   PLANT MOLECULAR BIOLOGY

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning

(2009) Sam Guoping Gu et al.   CHROMOSOMA

Chromatin Binding of SRp20 and ASF/SF2 and Dissociation from Mitotic Chromosomes Is Modulated by Histone H3 Serine 10 Phosphorylation

(2009) Rebecca J. Loomis et al.   MOLECULAR CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

(2009) Marieke Louwers et al.   Nature Protocols

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

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

Heterochromatin Protein 1 (HP1a) Positively Regulates Euchromatic Gene Expression through RNA Transcript Association and Interaction with hnRNPs in Drosophila

(2009) Lucia Piacentini et al.   PLoS Genetics

Histone H1 and its isoforms: Contribution to chromatin structure and function

(2008) Nicole Happel et al.   GENE

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

High-resolution statistical mapping reveals gene territories in live yeast

(2008) Axel B Berger et al.   NATURE METHODS

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

(2008) Yana V. Bernatavichute et al.   PLoS One

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology