Interferons reshape the 3D conformation and accessibility of macrophage chromatin

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

(2020) Gordana Wutz et al.   eLife

Serpentine: a flexible 2D binning method for differential Hi-C analysis

(2020) Lyam Baudry et al.   BIOINFORMATICS

Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion

(2020) Louisa Hill et al.   NATURE

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Computer vision for pattern detection in chromosome contact maps

(2020) Cyril Matthey-Doret et al.   Nature Communications

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions

(2019) Quen Cheng et al.   Scientific Reports

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

(2019) Nezar Abdennur et al.   BIOINFORMATICS

IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate macrophage activation

(2019) Kyuho Kang et al.   Nature Communications

A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription

(2019) Ekaterini Platanitis et al.   Nature Communications

Differential Activation of the Transcription Factor IRF1 Underlies the Distinct Immune Responses Elicited by Type I and Type III Interferons

(2019) Adriana Forero et al.   IMMUNITY

Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

(2019) Iris Steinparzer et al.   MOLECULAR CELL

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

(2018) Federico Comoglio et al.   GENOME RESEARCH

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Organizational principles of 3D genome architecture

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

The C-Terminal Transactivation Domain of STAT1 Has a Gene-Specific Role in Transactivation and Cofactor Recruitment

(2018) Matthias Parrini et al.   Frontiers in Immunology

Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation

(2018) Ekaterini Platanitis et al.   Frontiers in Immunology

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Canonical and Non-Canonical Aspects of JAK–STAT Signaling: Lessons from Interferons for Cytokine Responses

(2017) Andrea Majoros et al.   Frontiers in Immunology

Parsing the Interferon Transcriptional Network and Its Disease Associations

(2016) Sara Mostafavi et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation

(2016) David Langlais et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

STAT2 Is a Pervasive Cytokine Regulator due to Its Inhibition of STAT1 in Multiple Signaling Pathways

(2016) Johnathan Ho et al.   PLOS BIOLOGY

A dualcis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages

(2015) Alessandra Mancino et al.   GENES & DEVELOPMENT

Noncanonical Effects of IRF9 in Intestinal Inflammation: More than Type I and Type III Interferons

(2015) Isabella Rauch et al.   MOLECULAR AND CELLULAR BIOLOGY

Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex

(2015) Sebastian Wienerroither et al.   Cell Reports

Interferon-Stimulated Genes: A Complex Web of Host Defenses

(2014) William M. Schneider et al.   Annual Review of Immunology

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

(2014) Jill M. Dowen et al.   CELL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

The Human RVB Complex Is Required for Efficient Transcription of Type I Interferon-Stimulated Genes

(2013) L. Gnatovskiy et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2013) Fulai Jin et al.   NATURE

Constitutive Type I Interferon Modulates Homeostatic Balance through Tonic Signaling

(2012) Daniel J. Gough et al.   IMMUNITY

The JAK-STAT Pathway at Twenty

(2012) George R. Stark et al.   IMMUNITY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Inborn errors of anti-viral interferon immunity in humans

(2011) Vanessa Sancho-Shimizu et al.   Current Opinion in Virology

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

(2009) K. Adelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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