Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

(2021) Yuanlong Liu et al.   Nature Communications

On the existence and functionality of topologically associating domains

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

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

(2020) Joanna Achinger-Kawecka et al.   Nature Communications

Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment

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

Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation

(2020) Delphine Douillet et al.   NATURE GENETICS

CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation

(2020) Jingmei Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation

(2020) Marc A. J. Morgan et al.   NATURE GENETICS

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

(2019) Maria C. Donaldson-Collier et al.   NATURE GENETICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation

(2019) Aaron D. Viny et al.   Cell Stem Cell

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

(2019) Andrew R. Morton et al.   CELL

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

(2019) William A. Flavahan et al.   NATURE

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma

(2019) Richard P. Koche et al.   NATURE GENETICS

Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma

(2018) Elena Battistello et al.   BLOOD

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

NKL homeobox gene NKX2-2 is aberrantly expressed in Hodgkin lymphoma

(2018) Stefan Nagel et al.   Oncotarget

Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

(2017) Loren M. Lasko et al.   NATURE

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data

(2017) Mark Carty et al.   Nature Communications

Cryptic t(3;8)(q27;q24) and/or MYC-BCL6 linkage associated with MYC expression by immunohistochemistry is frequent in multiple-hit B-cell lymphomas

(2017) H Ohno et al.   Blood Cancer Journal

The CREBBP Acetyltransferase Is a Haploinsufficient Tumor Suppressor in B-cell Lymphoma

(2017) Jiyuan Zhang et al.   Cancer Discovery

The EMT transcription factor Zeb2 controls adult murine hematopoietic differentiation by regulating cytokine signaling

(2016) Jin Li et al.   BLOOD

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region

(2016) Karen L. Bunting et al.   IMMUNITY

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

Fast and accurate long-range phasing in a UK Biobank cohort

(2016) Po-Ru Loh et al.   NATURE GENETICS

UMI-4C for quantitative and targeted chromosomal contact profiling

(2016) Omer Schwartzman et al.   NATURE METHODS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Homeobox NKX2-3 promotes marginal-zone lymphomagenesis by activating B-cell receptor signalling and shaping lymphocyte dynamics

(2016) Eloy F. Robles et al.   Nature Communications

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Enhancer Sequence Variants and Transcription-Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B-Cell Lymphoma

(2015) Olivia I. Koues et al.   IMMUNITY

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

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

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Absence of canonical marks of active chromatin in developmentally regulated genes

(2015) Sílvia Pérez-Lluch et al.   NATURE GENETICS

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

(2015) R. J. H. Ryan et al.   Cancer Discovery

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

(2014) Suhas S.P. Rao et al.   CELL

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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

(2013) Eliezer Calo et al.   MOLECULAR CELL

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma

(2013) Jessica Okosun et al.   NATURE GENETICS

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas

(2012) G. D. Victora et al.   BLOOD

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

(2012) Wulan Deng et al.   CELL

Roles of BCL6 in normal and transformed germinal center B cells

(2012) Katia Basso et al.   IMMUNOLOGICAL REVIEWS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

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

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

EBV Immortalization of human B lymphocytes separated from small volumes of cryo-preserved whole blood

(2008) M. Amoli et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY