Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading

Dynamic enhancer function in the chromatin context

(2017) Ido Goldstein et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

(2016) Erin E. Swinstead et al.   BIOESSAYS

Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

(2016) Erin E. Swinstead et al.   CELL

Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration

(2016) Xuxu Sun et al.   Cell Stem Cell

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

(2016) Ido Goldstein et al.   GENOME RESEARCH

IL-6 pathway in the liver: From physiopathology to therapy

(2016) Dirk Schmidt-Arras et al.   JOURNAL OF HEPATOLOGY

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

(2016) E. L. Soucie et al.   SCIENCE

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo

(2015) Raymond E. Soccio et al.   CELL

Hepatocytes: a key cell type for innate immunity

(2015) Zhou Zhou et al.   Cellular & Molecular Immunology

Hepatocytes as Immunological Agents

(2015) Ian N. Crispe   JOURNAL OF IMMUNOLOGY

Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude via REV-ERB Loading

(2015) Bokai Zhu et al.   MOLECULAR CELL

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Integrative Genomic Signatures Of Hepatocellular Carcinoma Derived from Nonalcoholic Fatty Liver Disease

(2015) Itziar Frades et al.   PLoS One

The Activation of IL-1-Induced Enhancers Depends on TAK1 Kinase Activity and NF-κB p65

(2015) Liane Jurida et al.   Cell Reports

Chromatin structure and gene regulation: a dynamic view of enhancer function

(2015) Diana A Stavreva et al.   Nucleus

Chromatin structure and gene regulation: a dynamic view of enhancer function

(2015) Diana A Stavreva et al.   Nucleus

Metformin Suppresses Lipopolysaccharide (LPS)-induced Inflammatory Response in Murine Macrophages via Activating Transcription Factor-3 (ATF-3) Induction

(2014) Juyoung Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Endogenous intrahepatic IFNs and association with IFN-free HCV treatment outcome

(2014) Eric G. Meissner et al.   JOURNAL OF CLINICAL INVESTIGATION

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Role of interleukins in obesity: implications for metabolic disease

(2014) Mark A. Febbraio   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Proteomic and genomic studies of non-alcoholic fatty liver disease - clues in the pathogenesis

(2014) Jun Wei Lim   WORLD JOURNAL OF GASTROENTEROLOGY

Transcriptional Control of Inflammatory Responses

(2014) S. T. Smale et al.   Cold Spring Harbor Perspectives in Biology

Reprogramming the Chromatin Landscape: Interplay of the Estrogen and Glucocorticoid Receptors at the Genomic Level

(2013) T. B. Miranda et al.   CANCER RESEARCH

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

(2013) Lars Grøntved et al.   EMBO JOURNAL

Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling

(2013) Yu Qiao et al.   IMMUNITY

Peroxisome Proliferator-Activated Receptor   and C/EBP  Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading

(2013) M. S. Madsen et al.   MOLECULAR AND CELLULAR BIOLOGY

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

Hepatocyte-specific mutation of both NF-κB RelA and STAT3 abrogates the acute phase response in mice

(2012) Lee J. Quinton et al.   JOURNAL OF CLINICAL INVESTIGATION

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Hepatic acute phase proteins – Regulation by IL-6- and IL-1-type cytokines involving STAT3 and its crosstalk with NF-κB-dependent signaling

(2011) Johannes G. Bode et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

NF-κB in the liver—linking injury, fibrosis and hepatocellular carcinoma

(2011) Tom Luedde et al.   Nature Reviews Gastroenterology & Hepatology

Metabolic nuclear receptor signaling and the inflammatory acute phase response

(2011) Nicolas Venteclef et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Selective Transcription in Response to an Inflammatory Stimulus

(2010) Stephen T. Smale   CELL

NF-κB and STAT3 signaling hubs for lung innate immunity

(2010) Lee J. Quinton et al.   CELL AND TISSUE RESEARCH

Hepatic acute-phase proteins control innate immune responses during infection by promoting myeloid-derived suppressor cell function

(2010) Leif E. Sander et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Serum levels of proinflammatory cytokines interleukin-1β, interleukin-6, and tumor necrosis factor α in mixed cryoglobulinemia

(2009) Alessandro Antonelli et al.   ARTHRITIS AND RHEUMATISM

Persistently Activated Stat3 Maintains Constitutive NF-κB Activity in Tumors

(2009) Heehyoung Lee et al.   CANCER CELL

Mechanisms of the Hepatic Acute-Phase Response during Bacterial Pneumonia

(2009) L. J. Quinton et al.   INFECTION AND IMMUNITY

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Disturbed hepatic carbohydrate management during high metabolic demand in medium-chain acyl-CoA dehydrogenase (MCAD)-deficient mice

(2008) Hilde Herrema et al.   HEPATOLOGY