Three‐dimensional genome structure and function

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer

(2023) Jia-Ren Lin et al.   CELL

Chromosome territory reorganization through artificial chromosome fusion is compatible with cell fate determination and mouse development

(2023) Yuang Wang et al.   Cell Discovery

Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis

(2023) Dong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection

(2023) Mengbiao Guo et al.   Frontiers in Immunology

SARS-CoV-2 restructures host chromatin architecture

(2023) Ruoyu Wang et al.   Nature Microbiology

Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism

(2022) Martin Franke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation

(2022) Elizabeth Ing-Simmons et al.   CURRENT OPINION IN CELL BIOLOGY

Lamina-associated domains: Tethers and looseners

(2022) Stefano Giustino Manzo et al.   CURRENT OPINION IN CELL BIOLOGY

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

(2022) Dominic D. G. Owens et al.   Nature Communications

Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy

(2022) Yuliang Feng et al.   CIRCULATION

3D chromatin architecture and transcription regulation in cancer

(2022) Siwei Deng et al.   Journal of Hematology & Oncology

Differential cofactor dependencies define distinct types of human enhancers

(2022) Christoph Neumayr et al.   NATURE

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization

(2022) Weifang Liu et al.   Genes

Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer

(2022) Yongxing Du et al.   Advanced Science

High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation

(2022) Daniel Rico et al.   GENOME RESEARCH

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

(2022) Chiara Anania et al.   NATURE GENETICS

Interplay between regulatory elements and chromatin topology in cellular lineage determination

(2022) Vallari Shukla et al.   TRENDS IN GENETICS

Context-dependent enhancer function revealed by targeted inter-TAD relocation

(2022) Christopher Chase Bolt et al.   Nature Communications

Regulation of 3D Organization and Its Role in Cancer Biology

(2022) Anghui Peng et al.   Frontiers in Cell and Developmental Biology

Three‐dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development

(2022) Geng G. Tian et al.   Clinical and Translational Medicine

3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus

(2022) Ming Zhao et al.   ANNALS OF THE RHEUMATIC DISEASES

Subtype-specific 3D genome alteration in acute myeloid leukaemia

(2022) Jie Xu et al.   NATURE

The spatial organization of transcriptional control

(2022) Antonina Hafner et al.   NATURE REVIEWS GENETICS

Structural variants drive context-dependent oncogene activation in cancer

(2022) Zhichao Xu et al.   NATURE

Novel biological insights revealed from the investigation of multiscale genome architecture

(2022) Tianyi Ding et al.   Computational and Structural Biotechnology Journal

Patterns of de novo tandem repeat mutations and their role in autism

(2021) Ileena Mitra et al.   NATURE

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

(2021) Xin Luo et al.   CELL

Loop extrusion as a mechanism for formation of DNA damage repair foci

(2021) Coline Arnould et al.   NATURE

Decoding the organization, dynamics, and function of the 4D genome

(2021) Erin Aboelnour et al.   DEVELOPMENTAL CELL

Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release

(2021) Takeo Narita et al.   MOLECULAR CELL

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structures of the human Mediator and Mediator-bound preinitiation complex

(2021) Xizi Chen et al.   SCIENCE

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

(2021) Jinmi Choi et al.   eLife

Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies

(2021) Laurianne Scourzic et al.   Frontiers in Immunology

3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing

(2021) Lina Xu et al.   Acta Pharmaceutica Sinica B

Epigenetics and Heart Development

(2021) Rajani M. George et al.   Frontiers in Cell and Developmental Biology

Three-dimensional chromatin organization in brain function and dysfunction

(2021) Vishnu Dileep et al.   CURRENT OPINION IN NEUROBIOLOGY

Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus

(2021) Uirá Souto Melo et al.   HUMAN GENETICS

WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas

(2021) Mervi Aavikko et al.   HUMAN MOLECULAR GENETICS

High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis

(2021) Bo Ren et al.   Journal of Hematology & Oncology

Defining genome architecture at base-pair resolution

(2021) Peng Hua et al.   NATURE

Topological isolation of developmental regulators in mammalian genomes

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

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations

(2021) Christopher Chase Bolt et al.   Nature Communications

Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome

(2021) Patricia Garcia et al.   Nature Communications

The impact of chromosomal fusions on 3D genome folding and recombination in the germ line

(2021) Covadonga Vara et al.   Nature Communications

Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection

(2021) Dingbin Tang et al.   Cell Reports

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

(2021) Muhammad Muzammal Adeel et al.   Frontiers in Cell and Developmental Biology

Chromatin Conformation in Development and Disease

(2021) Ilias Boltsis et al.   Frontiers in Cell and Developmental Biology

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

(2021) Ana Rita Amândio et al.   GENES & DEVELOPMENT

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

(2021) Aneta Mikulasova et al.   GENOME RESEARCH

A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome

(2021) Luigia Cinque et al.   HUMAN GENETICS

The 3D Genome: From Structure to Function

(2021) Tapan Kumar Mohanta et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

(2021) Rebeca San Martin et al.   JOURNAL OF CELL BIOLOGY

Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells

(2021) Yezhang Zhu et al.   NUCLEIC ACIDS RESEARCH

Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer

(2021) Raquel Rouco et al.   Nature Communications

Cancer statistics, 2020

(2020) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

(2020) Amanda Khoury et al.   Nature Communications

Structure and mechanism of the RNA polymerase II transcription machinery

(2020) Allison C. Schier et al.   GENES & DEVELOPMENT

Pmp22 Super-enhancer Deletion Causes Tomacula Formation and Conduction Block in Peripheral Nerves

(2020) Harrison Pantera et al.   HUMAN MOLECULAR GENETICS

Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes

(2020) Mariana C.C. Silva et al.   JOURNAL OF CELL BIOLOGY

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

TFIID Enables RNA Polymerase II Promoter-Proximal Pausing

(2020) Charli B. Fant et al.   MOLECULAR CELL

Parental-to-embryo switch of chromosome organization in early embryogenesis

(2020) Samuel Collombet et al.   NATURE

KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes

(2020) Aditya Sankar et al.   NATURE CELL BIOLOGY

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia

(2020) Andreas Kloetgen et al.   NATURE GENETICS

Architectural proteins for the formation and maintenance of the 3D genome

(2020) Mengfan Li et al.   Science China-Life Sciences

Dynamics of the 4D genome during in vivo lineage specification and differentiation

(2020) A. Marieke Oudelaar et al.   Nature Communications

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

(2020) Ines Desanlis et al.   Nature Communications

Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs

(2020) Alexandra Bortnick et al.   Cell Reports

Three-dimensional chromatin in disease: What holds us together and what drives us apart?

(2020) Daniel M. Ibrahim et al.   CURRENT OPINION IN CELL BIOLOGY

HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by 3D genome structure remodeling in cervical cancer

(2020) Canhui Cao et al.   Journal of Genetics and Genomics

CTCF-mediated genome organization and leukemogenesis

(2020) Yi Qiu et al.   LEUKEMIA

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

(2020) Torahiko L. Higashi et al.   MOLECULAR CELL

Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

(2020) Leina Lu et al.   MOLECULAR CELL

Landscape of cohesin-mediated chromatin loops in the human genome

(2020) Fabian Grubert et al.   NATURE

Essential Roles of Cohesin STAG2 in Mouse Embryonic Development and Adult Tissue Homeostasis

(2020) Magali De Koninck et al.   Cell Reports

Insights into epigenetic patterns in mammalian early embryos

(2020) Ruimin Xu et al.   Protein & Cell

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

(2020) Suzanne E. de Bruijn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Self-Organizing Genome: Principles of Genome Architecture and Function

(2020) Tom Misteli   CELL

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder

(2020) Hannah K. Long et al.   Cell Stem Cell

Cell-type-specific 3D epigenomes in the developing human cortex

(2020) Michael Song et al.   NATURE

Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3

(2020) James E Collier et al.   eLife

Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming

(2020) Xiakun Chu et al.   Advanced Science

Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries

(2020) Aizhan Bizhanova et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The relationship between genome structure and function

(2020) A. Marieke Oudelaar et al.   NATURE REVIEWS GENETICS

Chromatin topology and the timing of enhancer function at theHoxDlocus

(2020) Eddie Rodríguez-Carballo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

(2020) Nan Zhang et al.   Nature Communications

3D landscape of Hepatitis B virus interactions with human chromatins

(2020) Bo Yang et al.   Cell Discovery

Three-dimensional chromatin organization in cardiac development and disease

(2020) Alessandro Bertero et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization

(2020) A Marieke Oudelaar et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

(2019) Kris G. Alavattam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

(2019) Lucas Patel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome

(2019) Bjørt K Kragesteen et al.   JOURNAL OF MEDICAL GENETICS

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

(2019) Yi-Rong Peng 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

Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo

(2019) Yoon Hee Jung et al.   MOLECULAR CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

(2019) Joke G. van Bemmel et al.   NATURE GENETICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Trim33 is required for appropriate development of pre-cardiogenic mesoderm

(2019) Sudha Rajderkar et al.   DEVELOPMENTAL BIOLOGY

Management strategies and future directions for systemic lupus erythematosus in adults

(2019) Laura Durcan et al.   LANCET

Structural Features of Transcription Factors Associating with Nucleosome Binding

(2019) Meilin Fernandez Garcia et al.   MOLECULAR CELL

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

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

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

(2019) Alexandra Despang et al.   NATURE GENETICS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

(2019) Christina Paliou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

(2019) Alessandro Bertero et al.   Nature Communications

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

(2019) Covadonga Vara et al.   Cell Reports

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

(2019) Nicole Ritter et al.   DEVELOPMENTAL CELL

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

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Molecular basis and biological function of variability in spatial genome organization

(2019) Elizabeth H. Finn et al.   SCIENCE

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos

(2019) Zhenhai Du et al.   MOLECULAR CELL

Key role for CTCF in establishing chromatin structure in human embryos

(2019) Xuepeng Chen et al.   NATURE

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells

(2019) Changya Chen et al.   Cell Reports

Herbal drug discovery for the treatment of nonalcoholic fatty liver disease

(2019) Tingting Yan et al.   Acta Pharmaceutica Sinica B

The rs626283 Variant in the MBOAT7 Gene is Associated with Insulin Resistance and Fatty Liver in Caucasian Obese Youth

(2018) Giuseppina R Umano et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Role of lysophosphatidic acid in the retinal pigment epithelium and photoreceptors

(2018) Grace E. Lidgerwood et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

(2018) Brian T. Weinert et al.   CELL

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

(2018) X. Shawn Liu et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Exit from Naive Pluripotency Induces a Transient X Chromosome Inactivation-like State in Males

(2018) Elsa J. Sousa et al.   Cell Stem Cell

Regulation of the neuropathy-associated Pmp22 gene by a distal super-enhancer

(2018) Harrison Pantera et al.   HUMAN MOLECULAR GENETICS

Genetics and epigenetics of NAFLD and NASH: Clinical impact

(2018) Mohammed Eslam et al.   JOURNAL OF HEPATOLOGY

Scc2 Is a Potent Activator of Cohesin’s ATPase that Promotes Loading by Binding Scc1 without Pds5

(2018) Naomi J. Petela et al.   MOLECULAR CELL

Pioneering the chromatin landscape

(2018) Kenneth S. Zaret   NATURE GENETICS

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sex reversal following deletion of a single distal enhancer ofSox9

(2018) Nitzan Gonen et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Enhancer Logic and Mechanics in Development and Disease

(2018) Ryan Rickels et al.   TRENDS IN CELL BIOLOGY

Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions

(2018) Kosuke Yamaguchi et al.   Cell Reports

A promoter interaction map for cardiovascular disease genetics

(2018) Lindsey E Montefiori et al.   eLife

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Chromatin Domains Go on Repeat in Disease

(2018) Benoit G. Bruneau et al.   CELL

Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis

(2018) Mengnan He et al.   International Journal of Biological Sciences

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

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

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation

(2018) Patrick Torbey et al.   PLoS Genetics

DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments

(2018) Yasuto Murayama   Nucleus

m6A mRNA modification regulates mammalian spermatogenesis

(2018) Zhen Lin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RUNX1 and the endothelial origin of blood

(2018) Long Gao et al.   EXPERIMENTAL HEMATOLOGY

Non-alcoholic fatty liver disease – A global public health perspective

(2018) Zobair M. Younossi   JOURNAL OF HEPATOLOGY

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

The Birth of the 3D Genome during Early Embryonic Development

(2018) Clemens B. Hug et al.   TRENDS IN GENETICS

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

(2018) Pierrick Moreau et al.   Nature Communications

Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9

(2018) Brittany Croft et al.   Nature Communications

Regulation of Chromatin Structure During Neural Development

(2018) Yusuke Kishi et al.   Frontiers in Neuroscience

Evolving concepts in dilated cardiomyopathy

(2017) Marco Merlo et al.   EUROPEAN JOURNAL OF HEART FAILURE

Long-distance interaction of the integrated HPV fragment with MYC gene and 8q24.22 region upregulating the allele-specific MYC expression in HeLa cells

(2017) Congle Shen et al.   INTERNATIONAL JOURNAL OF CANCER

Crossed wires: 3D genome misfolding in human disease

(2017) Heidi K. Norton et al.   JOURNAL OF CELL BIOLOGY

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

(2017) Gang Ren et al.   MOLECULAR CELL

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

(2017) Anja J Will et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment

(2017) Ravi Boya et al.   NUCLEIC ACIDS RESEARCH

Changes in chromosome territory position within the nucleus reflect alternations in gene expression related to embryonic lineage specification

(2017) Maciej Orsztynowicz et al.   PLoS One

DNA methylation and DNA methyltransferases

(2017) John R. Edwards et al.   Epigenetics & Chromatin

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

(2017) Stephan Nothjunge et al.   Nature Communications

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

Scc2/Nipbl hops between chromosomal cohesin rings after loading

(2017) James Rhodes et al.   eLife

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

(2016) Emily M. Smith et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Control of Meiotic Crossovers: From Double-Strand Break Formation to Designation

(2016) Stephen Gray et al.   Annual Review of Genetics

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex

(2016) Philip J. Robinson et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

SOX9 and the many facets of its regulation in the chondrocyte lineage

(2016) Véronique Lefebvre et al.   CONNECTIVE TISSUE RESEARCH

Gene regulation and chromatin organization: relevance of cohesin mutations to human disease

(2016) Erwan Watrin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Cohesin acetylation and Wapl‐Pds5 oppositely regulate translocation of cohesin along DNA

(2016) Mai Kanke et al.   EMBO JOURNAL

A role for HOX13 proteins in the regulatory switch between TADs at theHoxDlocus

(2016) Leonardo Beccari et al.   GENES & DEVELOPMENT

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

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

(2016) Guillaume Andrey et al.   GENOME RESEARCH

Looking beyond the genes: the role of non-coding variants in human disease

(2016) Malte Spielmann et al.   HUMAN MOLECULAR GENETICS

Structural Basis and IP 6 Requirement for Pds5-Dependent Cohesin Dynamics

(2016) Zhuqing Ouyang et al.   MOLECULAR CELL

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

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

(2016) Pratiti Bandopadhayay et al.   NATURE GENETICS

Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

(2016) Hao Yuan Kueh et al.   NATURE IMMUNOLOGY

Epidemiology and aetiology of heart failure

(2016) Boback Ziaeian et al.   Nature Reviews Cardiology

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis

(2016) Daniel S. Neems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

(2016) Muhammad A. Zabidi et al.   TRENDS IN GENETICS

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

(2016) Mark A. Le Gros et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Identification of the fourth duplication of upstreamIHHregulatory elements, in a family with craniosynostosis Philadelphia type, helps to define the phenotypic characterization of these regulatory elements

(2015) Eva Barroso et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

X-chromosome inactivation: new insights into cis and trans regulation

(2015) Rafael Galupa et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus

(2015) Andrew J. Fritz et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Copy number variation of two separate regulatory regions upstream ofSOX9causes isolated 46,XY or 46,XX disorder of sex development

(2015) Gwang-Jin Kim et al.   JOURNAL OF MEDICAL GENETICS

DDX60L Is an Interferon-Stimulated Gene Product Restricting Hepatitis C Virus Replication in Cell Culture

(2015) Oliver Grünvogel et al.   JOURNAL OF VIROLOGY

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

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

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Differential contribution ofcis-regulatory elements to higher order chromatin structure and expression of theCFTRlocus

(2015) Rui Yang et al.   NUCLEIC ACIDS RESEARCH

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meiotic Recombination: The Essence of Heredity

(2015) Neil Hunter   Cold Spring Harbor Perspectives in Biology

Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness

(2015) S. Kmoch et al.   Nature Communications

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

(2015) Zeba Wunderlich et al.   Cell Reports

Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition

(2014) Marcel Kool et al.   CANCER CELL

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo

(2014) M. Werber et al.   DEVELOPMENT

The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function

(2014) Sören Boller et al.   IMMUNOLOGICAL REVIEWS

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

The Scc2–Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions

(2014) Lidia Lopez-Serra et al.   NATURE GENETICS

A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia

(2014) Daniel Herranz et al.   NATURE MEDICINE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

Developmental and genetic perspectives on Pierre Robin sequence

(2013) Tiong Yang Tan et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies

(2013) Alexander R. Ball et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structural variations, the regulatory landscape of the genome and their alteration in human disease

(2013) Malte Spielmann et al.   BIOESSAYS

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

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

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

(2013) Phillip Grote et al.   DEVELOPMENTAL CELL

Liebenberg syndrome is caused by a deletion upstream to the PITX1 gene resulting in transformation of the upper limbs to reflect lower limb characteristics

(2013) Mohammad M. Al-Qattan et al.   GENE

Mutation Spectrum and Genotype-Phenotype Correlation in Cornelia de Lange Syndrome

(2013) Linda Mannini et al.   HUMAN MUTATION

The Liebenberg syndrome: in depth analysis of the original family

(2013) U. Mennen et al.   Journal of Hand Surgery-European Volume

Biochemical reconstitution of topological DNA binding by the cohesin ring

(2013) Yasuto Murayama et al.   NATURE

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

(2013)   NATURE GENETICS

The Unstable Repeats—Three Evolving Faces of Neurological Disease

(2013) David L. Nelson et al.   NEURON

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

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

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

(2013) G. Andrey et al.   SCIENCE

Homeotic Arm-to-Leg Transformation Associated with Genomic Rearrangements at the PITX1 Locus

(2012) Malte Spielmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) Tom Sexton et al.   CELL

The immunoglobulin heavy chain locus: genetic variation, missing data and implications for human disease

(2012) C T Watson et al.   GENES AND IMMUNITY

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Distant Activation of Transcription: Mechanisms of Enhancer Action

(2012) O. I. Kulaeva et al.   MOLECULAR AND CELLULAR BIOLOGY

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones 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

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

(2012) Hebing Chen et al.   PLoS One

Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus

(2012) T. Montavon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo 5q14.3 translocation 121.5-kb upstream of MEF2C in a patient with severe intellectual disability and early-onset epileptic encephalopathy

(2011) Hirotomo Saitsu et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications

(2011) S. M. Hattangadi et al.   BLOOD

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

Sox9 function in craniofacial development and disease

(2011) Young-Hoon Lee et al.   GENESIS

Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity

(2011) T. Xiao et al.   MOLECULAR AND CELLULAR BIOLOGY

Global DNA Demethylation During Mouse Erythropoiesis in Vivo

(2011) J. R. Shearstone et al.   SCIENCE

Formation of mammalian erythrocytes: chromatin condensation and enucleation

(2011) Peng Ji et al.   TRENDS IN CELL BIOLOGY

Developmental Control of Oocyte Maturation and Egg Activation in Metazoan Models

(2011) J. R. Von Stetina et al.   Cold Spring Harbor Perspectives in Biology

Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells

(2011) Tatyana B Nesterova et al.   Epigenetics & Chromatin

Multifactorial Origins of Heart and Gut Defects in nipbl-Deficient Zebrafish, a Model of Cornelia de Lange Syndrome

(2011) Akihiko Muto et al.   PLOS BIOLOGY

Copy-Number Variations Involving the IHH Locus Are Associated with Syndactyly and Craniosynostosis

(2010) Eva Klopocki et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genotype-phenotype analysis of the branchio-oculo-facial syndrome

(2010) Jeff M. Milunsky et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Genotype-phenotype correlation in eight new patients with a deletion encompassing 2q31.1

(2010) Diana Mitter et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Functional Analysis of CTCF During Mammalian Limb Development

(2010) Natalia Soshnikova et al.   DEVELOPMENTAL CELL

Mutations in MEF2C from the 5q14.3q15 microdeletion syndrome region are a frequent cause of severe mental retardation and diminish MECP2 and CDKL5 expression

(2010) Markus Zweier et al.   HUMAN MUTATION

Understanding follicle growth in vivo

(2010) O. Oktem et al.   HUMAN REPRODUCTION

2q31.1 microdeletion syndrome: redefining the associated clinical phenotype

(2010) B. Dimitrov et al.   JOURNAL OF MEDICAL GENETICS

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Mechanisms of trinucleotide repeat instability during human development

(2010) Cynthia T. McMurray   NATURE REVIEWS GENETICS

Repeat expansion disease: progress and puzzles in disease pathogenesis

(2010) Albert R. La Spada et al.   NATURE REVIEWS GENETICS

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

(2010) Joke G. van Bemmel et al.   PLoS One

Loss of lysophosphatidylcholine acyltransferase 1 leads to photoreceptor degeneration in rd11 mice

(2010) J. S. Friedman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

A novel microdeletion syndrome involving 5q14.3-q15: clinical and molecular cytogenetic characterization of three patients

(2009) Hartmut Engels et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

MEF2C haploinsufficiency caused by either microdeletion of the 5q14.3 region or mutation is responsible for severe mental retardation with stereotypic movements, epilepsy and/or cerebral malformations

(2009) N. Le Meur et al.   JOURNAL OF MEDICAL GENETICS

Building Sister Chromatid Cohesion: Smc3 Acetylation Counteracts an Antiestablishment Activity

(2009) Benjamin D. Rowland et al.   MOLECULAR CELL

Neuroscience: Glia — more than just brain glue

(2009) Nicola J. Allen et al.   NATURE

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Distinctive chromatin in human sperm packages genes for embryo development

(2009) Saher Sue Hammoud et al.   NATURE

Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia

(2009) Ingo Kurth et al.   NATURE GENETICS

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

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

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

Multiple Organ System Defects and Transcriptional Dysregulation in the Nipbl+/− Mouse, a Model of Cornelia de Lange Syndrome

(2009) Shimako Kawauchi et al.   PLoS Genetics

TFAP2A Mutations Result in Branchio-Oculo-Facial Syndrome

(2008) Jeff M. Milunsky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cohesin and Human Disease

(2008) Jinglan Liu et al.   Annual Review of Genomics and Human Genetics

Pancreatic Cancer

(2008) Anirban Maitra et al.   Annual Review of Pathology-Mechanisms of Disease

CTCF regulates cell cycle progression of αβ T cells in the thymus

(2008) Helen Heath et al.   EMBO JOURNAL