Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription

(2018) Yong Hoon Kim et al.   SCIENCE

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

A UTX-MLL4-p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription

(2017) Shu-Ping Wang et al.   MOLECULAR CELL

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

The immunology of atherosclerosis

(2017) Anton Gisterå et al.   Nature Reviews Nephrology

Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation

(2017) Yasuharu Kanki et al.   NUCLEIC ACIDS RESEARCH

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells

(2017) Nicholas T Hogan et al.   eLife

TADtool: visual parameter identification for TAD-calling algorithms

(2016) Kai Kruse et al.   BIOINFORMATICS

MicroRNA Regulation of Atherosclerosis

(2016) Mark W. Feinberg et al.   CIRCULATION RESEARCH

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

Crucial Role of the Aryl Hydrocarbon Receptor (AhR) in Indoxyl Sulfate-Induced Vascular Inflammation

(2016) Shunsuke Ito et al.   Journal of Atherosclerosis and Thrombosis

UTX demethylase activity is required for satellite cell–mediated muscle regeneration

(2016) Hervé Faralli et al.   JOURNAL OF CLINICAL INVESTIGATION

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells

(2016) Semir Beyaz et al.   NATURE IMMUNOLOGY

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells

(2015) Kazuki Kurimoto et al.   Cell Stem Cell

Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers

(2015) Søren Fisker Schmidt et al.   GENOME RESEARCH

Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice

(2015) Rene C. Adam et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

(2015) Nasun Hah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

(2015) Jan J Zylicz et al.   eLife

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

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

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) Jill M. Dowen et al.   CELL

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

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

The Histone H3 Lysine 9 Methyltransferases G9a and GLP Regulate Polycomb Repressive Complex 2-Mediated Gene Silencing

(2014) Chiara Mozzetta et al.   MOLECULAR CELL

Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia

(2014) Panagiotis Ntziachristos et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma

(2014) Rintaro Hashizume et al.   NATURE MEDICINE

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

(2014) Robert Huether et al.   Nature Communications

Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements

(2014) Tsuyoshi Inoue et al.   GENOME BIOLOGY

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

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

(2013) Fulai Jin et al.   NATURE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response

(2012) Terry C. Fang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Dynamic Change of Chromatin Conformation in Response to Hypoxia Enhances the Expression of GLUT3 (SLC2A3) by Cooperative Interaction of Hypoxia-Inducible Factor 1 and KDM3A

(2012) I. Mimura et al.   MOLECULAR AND CELLULAR BIOLOGY

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

(2012) Laurens Kruidenier et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions

(2012) Ryo Nakaki et al.   NUCLEIC ACIDS RESEARCH

UTX, a Histone H3-Lysine 27 Demethylase, Acts as a Critical Switch to Activate the Cardiac Developmental Program

(2011) Seunghee Lee et al.   DEVELOPMENTAL CELL

Epigenetically coordinated GATA2 binding is necessary for endothelium-specificendomucinexpression

(2011) Yasuharu Kanki et al.   EMBO JOURNAL

Genome-Wide Approaches Reveal Functional Interleukin-4-Inducible STAT6 Binding to the Vascular Cell Adhesion Molecule 1 Promoter

(2011) H. Tozawa et al.   MOLECULAR AND CELLULAR BIOLOGY

Progress and challenges in translating the biology of atherosclerosis

(2011) Peter Libby et al.   NATURE

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

(2011) Yaoting Gui et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Increased expression of histone demethylase JHDM1D under nutrient starvation suppresses tumor growth via down-regulating angiogenesis

(2011) T. Osawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis

(2010) Shayesta Seenundun et al.   EMBO JOURNAL

KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development

(2010) Y.-i. Tsukada et al.   GENES & DEVELOPMENT

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

(2010) Gillian L. Dalgliesh et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

(2009) Francesca De Santa et al.   EMBO JOURNAL

Cutting Edge: TNF-Induced MicroRNAs Regulate TNF-Induced Expression of E-Selectin and Intercellular Adhesion Molecule-1 on Human Endothelial Cells: Feedback Control of Inflammation

(2009) Yajaira Suárez et al.   JOURNAL OF IMMUNOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer

(2009) Gijs van Haaften et al.   NATURE GENETICS

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases

(2009) John R Horton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY