Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5′ and 3′ flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion

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

(2019) Ekaterini Platanitis et al.   Nature Communications

DNA-binding landscape of IRF3, IRF5 and IRF7 dimers: implications for dimer-specific gene regulation

(2018) Kellen K Andrilenas et al.   NUCLEIC ACIDS RESEARCH

Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function

(2018) Srinivasan Rengachari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

B Cell-Intrinsic Role for IRF5 in TLR9/BCR-Induced Human B Cell Activation, Proliferation, and Plasmablast Differentiation

(2018) Saurav De et al.   Frontiers in Immunology

Interferon Regulatory Factor 9 Structure and Regulation

(2018) Alvin Paul et al.   Frontiers in Immunology

IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection

(2018) Kwan T. Chow et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation

(2018) Ekaterini Platanitis et al.   Frontiers in Immunology

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

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

The emerging role of interferon regulatory factor 9 in the antiviral host response and beyond

(2016) Tamara Suprunenko et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Specificity and Function of IRF Family Transcription Factors: Insights from Genomics

(2016) Alessandra Mancino et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

Interferon regulatory factors: at the crossroads of immunity, metabolism, and disease

(2015) Guang-Nian Zhao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Using epigenomics data to predict gene expression in lung cancer

(2015) Jeffery Li et al.   BMC BIOINFORMATICS

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

(2015) Alessandra Mancino et al.   GENES & DEVELOPMENT

TLR3-Mediated CD8+Dendritic Cell Activation Is Coupled with Establishment of a Cell-Intrinsic Antiviral State

(2015) Lajos Széles et al.   JOURNAL OF IMMUNOLOGY

Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA

(2015) Diana R. Ourthiague et al.   JOURNAL OF LEUKOCYTE 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

Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation

(2015) Arne W. Mould et al.   PLoS Genetics

Chromatin Contributions to the Regulation of Innate Immunity

(2014) Stephen T. Smale et al.   Annual Review of Immunology

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

(2014) B. Daniel et al.   GENES & DEVELOPMENT

IRF5:RelA Interaction Targets Inflammatory Genes in Macrophages

(2014) David G. Saliba et al.   Cell Reports

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

IRF-5 and NF-κB p50 co-regulate IFN-β and IL-6 expression in TLR9-stimulated human plasmacytoid dendritic cells

(2013) Folkert Steinhagen et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Extensive Cooperation of Immune Master Regulators IRF3 and NFκB in RNA Pol II Recruitment and Pause Release in Human Innate Antiviral Transcription

(2013) Jonathan E. Freaney et al.   Cell Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes

(2012) N. Henriette Uhlenhaut et al.   MOLECULAR CELL

Compensatory dendritic cell development mediated by BATF–IRF interactions

(2012) Roxane Tussiwand et al.   NATURE

BATF–JUN is critical for IRF4-mediated transcription in T cells

(2012) Peng Li et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Cross-interference of RLR and TLR signaling pathways modulates antibacterial T cell responses

(2012) Hideo Negishi et al.   NATURE IMMUNOLOGY

A Genomic Regulatory Element That Directs Assembly and Function of Immune-Specific AP-1-IRF Complexes

(2012) E. Glasmacher et al.   SCIENCE

IRF5 promotes inflammatory macrophage polarization and TH1-TH17 responses

(2011) Thomas Krausgruber et al.   NATURE IMMUNOLOGY

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

(2011) Trevor Siggers et al.   NATURE IMMUNOLOGY

Interferon-stimulated genes and their antiviral effector functions

(2011) John W Schoggins et al.   Current Opinion in Virology

Regulation of immunity and oncogenesis by the IRF transcription factor family

(2010) David Savitsky et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Selective Transcription in Response to an Inflammatory Stimulus

(2010) Stephen T. Smale   CELL

Bcl-6 and NF- B cistromes mediate opposing regulation of the innate immune response

(2010) G. D. Barish et al.   GENES & DEVELOPMENT

Transcription Factor Redundancy Ensures Induction of the Antiviral State

(2010) Sonja Schmid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Contribution of IRF5 in B cells to the development of murine SLE-like disease through its transcriptional control of the IgG2a locus

(2010) D. A. Savitsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

The IRF Family Transcription Factors in Immunity and Oncogenesis

(2008) Tomohiko Tamura et al.   Annual Review of Immunology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY