Decoding the role of chromatin architecture in development: coming closer to the end of the tunnel

Arabidopsis guard cell integrity involves the epigenetic stabilization of theFLPandFAMAtranscription factor genes

(2014) EunKyoung Lee et al.   PLANT JOURNAL

The epigenome in pluripotency and differentiation

(2014) Rathi D Thiagarajan et al.   Epigenomics

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

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

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

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem Cell

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

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

(2013) Andrew S Belmont   CURRENT OPINION IN CELL BIOLOGY

Long non-coding RNAs: modulators of nuclear structure and function

(2013) Jan H Bergmann et al.   CURRENT OPINION IN CELL BIOLOGY

Identical cells with different 3D genomes; cause and consequences?

(2013) Peter HL Krijger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Twisting chromatin in stem cells

(2013) Paul Ginno et al.   EMBO JOURNAL

Physical clustering of FLC alleles during Polycomb-mediated epigenetic silencing in vernalization

(2013) S. Rosa et al.   GENES & DEVELOPMENT

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

(2013) Stefan Grob et al.   GENOME BIOLOGY

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng 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

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

(2012) F. A. Steiner et al.   GENOME RESEARCH

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

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

RNA-based regulation of pluripotency

(2012) Jane E. Wright et al.   TRENDS IN GENETICS

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Pairing of lacO tandem repeats in Arabidopsis thaliana nuclei requires the presence of hypermethylated, large arrays at two chromosomal positions, but does not depend on H3-lysine-9-dimethylation

(2011) Gabriele Jovtchev et al.   CHROMOSOMA

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

RopGEF7Regulates PLETHORA-Dependent Maintenance of the Root Stem Cell Niche inArabidopsis

(2011) Min Chen et al.   PLANT CELL

Chromatin Regulatory Mechanisms in Pluripotency

(2010) Julie A. Lessard et al.   Annual Review of Cell and Developmental Biology

Chromatin plasticity and genome organization in pluripotent embryonic stem cells

(2010) Anna Mattout et al.   CURRENT OPINION IN CELL BIOLOGY

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Epigenetic modifications in pluripotent and differentiated cells

(2010) Alexander Meissner   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin Remodeling in Stem Cell Maintenance in Arabidopsis thaliana

(2009) Wen-Hui Shen et al.   Molecular Plant

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Tissue- and Expression Level-Specific Chromatin Looping at Maize b1 Epialleles

(2009) M. Louwers et al.   PLANT CELL

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

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

The stem cell—Chromatin connection

(2009) Yi Sang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Size and number of tandem repeat arrays can determine somatic homologous pairing of transgene loci mediated by epigenetic modifications in Arabidopsis thaliana nuclei

(2008) Gabriele Jovtchev et al.   CHROMOSOMA

Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis

(2008) Faye M. Rosin et al.   PLANT JOURNAL