Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

(2022) Miguel Martinez-Ara et al.   MOLECULAR CELL

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

BRD2 compartmentalizes the accessible genome

(2022) Liangqi Xie et al.   NATURE GENETICS

Compatibility rules of human enhancer and promoter sequences

(2022) Drew T. Bergman et al.   NATURE

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands

(2021) Daniel N. Weinberg et al.   NATURE GENETICS

Role of FAT1 in health and disease (Review)

(2021) Zizhen Peng et al.   Oncology Letters

Transcriptional enhancers and their communication with gene promoters

(2021) Helen Ray-Jones et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Three-dimensional folding dynamics of the Xenopus tropicalis genome

(2021) Longjian Niu et al.   NATURE GENETICS

Topological isolation of developmental regulators in mammalian genomes

(2021) Hua-Jun Wu et al.   Nature Communications

Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation

(2021) Moritz Bauer et al.   Nature Communications

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

(2021) Yuan Yin et al.   Nature Communications

Local rewiring of genome–nuclear lamina interactions by transcription

(2020) Laura Brueckner et al.   EMBO JOURNAL

Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases

(2020) Uirá Souto Melo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment

(2020) Celeste D. Rosencrance et al.   MOLECULAR CELL

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Comparative transcriptomics of primary cells in vertebrates

(2020) Tanvir Alam et al.   GENOME RESEARCH

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

(2020) Mattia Conte et al.   Nature Communications

Identification of distinct loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development

(2020) Masaki Yagi et al.   Nature Communications

Cell cycle dynamics of lamina‐associated DNA

(2020) Tom van Schaik et al.   EMBO REPORTS

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality

(2020) Francisca M. Real et al.   SCIENCE

A map of cis-regulatory elements and 3D genome structures in zebrafish

(2020) Hongbo Yang et al.   NATURE

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

(2020) Ning Qing Liu et al.   NATURE GENETICS

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Predicting enhancers in mammalian genomes using supervised hidden Markov models

(2019) Tobias Zehnder et al.   BMC BIOINFORMATICS

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

(2019) Magdalena Laugsch et al.   Cell Stem Cell

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Eutherian-specific gene TRIML2 attenuates inflammation in the evolution of placentation

(2019) Xuzhe Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-specific activities of the Fat1 cadherin cooperate to control neuromuscular morphogenesis

(2018) Françoise Helmbacher   PLOS BIOLOGY

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

(2017) Peng Huang et al.   GENES & DEVELOPMENT

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

(2017) Michael I. Robson et al.   GENOME RESEARCH

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

(2017) Nathan Harmston et al.   Nature Communications

Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF

(2017) Ivana Jerković et al.   PLoS Genetics

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

(2017) Rafael D. Acemel et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

(2016) Guillaume Andrey et al.   GENOME RESEARCH

Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis

(2016) Michael I. Robson et al.   MOLECULAR CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

(2015) Frank Jühling et al.   GENOME RESEARCH

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy

(2015) Graeme Ball et al.   Scientific Reports

Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice

(2015) Katerina Kraft et al.   Cell Reports

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

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

(2014) Suhas S.P. Rao et al.   CELL

Mapping the Shh long-range regulatory domain

(2014) E. Anderson et al.   DEVELOPMENT

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Pierre Therizols et al.   SCIENCE

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage

(2013) Mirang Kim et al.   HUMAN MOLECULAR GENETICS

Sleeping Giants: Emerging Roles for the Fat Cadherins in Health and Disease

(2013) Elham Sadeqzadeh et al.   MEDICINAL RESEARCH REVIEWS

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Phylogenetic and molecular evolution of the ADAM (A Disintegrin And Metalloprotease) gene family from Xenopus tropicalis, to Mus musculus, Rattus norvegicus, and Homo sapiens

(2012) Jiaoyue Long et al.   GENE

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rex1/Zfp42 as an epigenetic regulator for genomic imprinting

(2011) Jeong Do Kim et al.   HUMAN MOLECULAR GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

(2010) Yingying Zhang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus

(2009) Mario Nicodemi et al.   BIOPHYSICAL JOURNAL

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Epigenetic Temporal Control of Mouse Hox Genes in Vivo

(2009) N. Soshnikova et al.   SCIENCE

Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination

(2008) Mats G.L. Gustafsson et al.   BIOPHYSICAL JOURNAL

Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells

(2008) Shinji Masui et al.   BMC DEVELOPMENTAL BIOLOGY

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy

(2008) L. Schermelleh et al.   SCIENCE

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics