Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region

Comparative Transcriptomics Analyses in Livers of Mice, Humans, and Humanized Mice Define Human-Specific Gene Networks

(2020) Chengfei Jiang et al.   Cells

HEPATIC TRANSCRIPTOME SIGNATURES IN PATIENTS WITH VARYING DEGREES OF NON-ALCOHOLIC FATTY LIVER DISEASE COMPARED TO HEALTHY NORMAL-WEIGHT INDIVIDUALS

(2019) Malte P Suppli et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

(2019) Jean-Pierre Etchegaray et al.   MOLECULAR CELL

Expression and function of FRA1 protein in tumors

(2019) Xiaoyan Jiang et al.   MOLECULAR BIOLOGY REPORTS

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Interleukin-6 Reduces β-Cell Oxidative Stress by Linking Autophagy With the Antioxidant Response

(2018) Michelle R. Marasco et al.   DIABETES

Impact of silencing hepatic SREBP-1 on insulin signaling

(2018) Victoria Jideonwo et al.   PLoS One

Role of the Circadian Clock in the Metabolic Syndrome and Nonalcoholic Fatty Liver Disease

(2018) Akshay Shetty et al.   DIGESTIVE DISEASES AND SCIENCES

Loss of ATF3 exacerbates liver damage through the activation of mTOR/p70S6K/ HIF-1α signaling pathway in liver inflammatory injury

(2018) Qiang Zhu et al.   Cell Death & Disease

Ras-ERK1/2 signaling contributes to the development of colorectal cancer via regulating H3K9ac

(2018) Peng Tian et al.   BMC CANCER

Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation

(2017) Leah A. Gates et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation

(2017) Latifa Bakiri et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis

(2017) Maria Ryaboshapkina et al.   Scientific Reports

FOXO transcription factors protect against the diet-induced fatty liver disease

(2017) Xiaoyan Pan et al.   Scientific Reports

Non-alcoholic fatty liver disease and risk of type 2 diabetes

(2016) S. Lallukka et al.   BEST PRACTICE & RESEARCH CLINICAL ENDOCRINOLOGY & METABOLISM

Liver-Specific Silencing of Lipin1 Reduces Fat Mass as Well as Hepatic Triglyceride Biosynthesis in Mice

(2016) Kazuaki Kajimoto et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

H3K9 acetylation change patterns in rats after exposure to traffic-related air pollution

(2016) Rui Ding et al.   ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY

Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes

(2016) Zobair M. Younossi et al.   HEPATOLOGY

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Circadian physiology of metabolism

(2016) Satchidananda Panda   SCIENCE

Gene targets of mouse miR-709: regulation of distinct pools

(2016) Sneha Surendran et al.   Scientific Reports

ATP-Citrate Lyase Controls a Glucose-to-Acetate Metabolic Switch

(2016) Steven Zhao et al.   Cell Reports

Chromatin Modifications Associated With Diabetes and Obesity

(2015) Dustin E. Schones et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Glycolysis-Mediated Changes in Acetyl-CoA and Histone Acetylation Control the Early Differentiation of Embryonic Stem Cells

(2015) Arieh Moussaieff et al.   Cell Metabolism

Epigenetics and Metabolism

(2015) S. T. Keating et al.   CIRCULATION RESEARCH

Altered hepatic gene expression in nonalcoholic fatty liver disease is associated with lower hepatic n-3 and n-6 polyunsaturated fatty acids

(2015) Bianca M. Arendt et al.   HEPATOLOGY

Global histone modifications in Fumonisin B1 exposure in rat kidney epithelial cells

(2015) Duygu Sancak et al.   TOXICOLOGY IN VITRO

Age-dependent clinical prognostic value of histone modifications in colorectal cancer

(2015) Inès J. Goossens-Beumer et al.   Translational Research

Regulation of Steatohepatitis and PPARγ Signaling by Distinct AP-1 Dimers

(2014) Sebastian C. Hasenfuss et al.   Cell Metabolism

Open Chromatin Profiling in Mice Livers Reveals Unique Chromatin Variations Induced by High Fat Diet

(2014) Amy Leung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sterol Regulatory Element-binding Protein-1 (SREBP-1) Is Required to Regulate Glycogen Synthesis and Gluconeogenic Gene Expression in Mouse Liver

(2014) Rafaela Ruiz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Vaspin inhibits kallikrein 7 by serpin mechanism

(2013) John T. Heiker et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Activator protein 1 transcription factor fos-related antigen 1 (fra-1) is dispensable for murine liver fibrosis, but modulates xenobiotic metabolism

(2013) Sebastian C. Hasenfuss et al.   HEPATOLOGY

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Sexually Dimorphic Genome-Wide Binding of Retinoid X Receptor alpha (RXRα) Determines Male-Female Differences in the Expression of Hepatic Lipid Processing Genes in Mice

(2013) Astrid Kosters et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Lactate, a product of glycolytic metabolism, inhibits histone deacetylase activity and promotes changes in gene expression

(2012) Tom Latham et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

(2011) Yun Chen et al.   BMC GENOMICS

Longitudinal association between IGFBP-1 levels and parameters of the metabolic syndrome in obese children before and after weight loss

(2011) Thomas Reinehr et al.   International Journal of Pediatric Obesity

Regulator of G Protein Signaling (RGS16) Inhibits Hepatic Fatty Acid Oxidation in a Carbohydrate Response Element-binding Protein (ChREBP)-dependent Manner

(2011) Victor Pashkov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

Evidence for the role of oxidative stress in the acetylation of histone H3 by ethanol in rat hepatocytes

(2010) Mahua Choudhury et al.   ALCOHOL

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

(2010) Anton Kratz et al.   BMC GENOMICS

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

Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes

(2010) Biliana Marcheva et al.   NATURE

Risk of Cardiovascular Disease in Patients with Nonalcoholic Fatty Liver Disease

(2010) Giovanni Targher et al.   NEW ENGLAND JOURNAL OF MEDICINE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE

The Emerging Role of Nuclear Receptor RORα and Its Crosstalk with LXR in Xeno- and Endobiotic Gene Regulation

(2008) Taira Wada et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE