Dynamic enhancers control skeletal muscle identity and reprogramming

ERRγ Promotes Angiogenesis, Mitochondrial Biogenesis, and Oxidative Remodeling in PGC1α/β-Deficient Muscle

(2018) Weiwei Fan et al.   Cell Reports

Long non-coding RNA ChRO1 facilitates ATRX/DAXX-dependent H3.3 deposition for transcription-associated heterochromatin reorganization

(2018) Jinyoung Park et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of motif activity and gene expression changes of transcription factors

(2017) Jesper Grud Skat Madsen et al.   GENOME RESEARCH

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

(2017) Songjoon Baek et al.   Cell Reports

Omics and Exercise: Global Approaches for Mapping Exercise Biological Networks

(2017) Nolan J. Hoffman   Cold Spring Harbor Perspectives in Medicine

Role of Nuclear Receptors in Exercise-Induced Muscle Adaptations

(2017) Barbara Kupr et al.   Cold Spring Harbor Perspectives in Medicine

Health Benefits of Exercise

(2017) Gregory N. Ruegsegger et al.   Cold Spring Harbor Perspectives in Medicine

Adipocyte glucocorticoid receptor is important in lipolysis and insulin resistance due to exogenous steroids, but not insulin resistance caused by high fat feeding

(2017) Yachen Shen et al.   Molecular Metabolism

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

Exercise-like effects by Estrogen-related receptor-gamma in muscle do not prevent insulin resistance in db/db mice

(2016) Pierre-Marie Badin et al.   Scientific Reports

MyoD Regulates Skeletal Muscle Oxidative Metabolism Cooperatively with Alternative NF-κB

(2016) Jonathan Shintaku et al.   Cell Reports

PGC-1α modulates necrosis, inflammatory response, and fibrotic tissue formation in injured skeletal muscle

(2016) Ivana Dinulovic et al.   Skeletal Muscle

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits

(2015) P. Darrell Neufer et al.   Cell Metabolism

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Tbx15 controls skeletal muscle fibre-type determination and muscle metabolism

(2015) Kevin Y. Lee et al.   Nature Communications

The multiple universes of estrogen-related receptor α and γ in metabolic control and related diseases

(2014) Étienne Audet-walsh et al.   ACTA PHARMACOLOGICA SINICA

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis

(2014) Margaret Buckingham et al.   DEVELOPMENTAL CELL

Muscle-Specific Overexpression of PGC-1α Does Not Augment Metabolic Improvements in Response to Exercise and Caloric Restriction

(2014) Kari E. Wong et al.   DIABETES

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

(2014) Maléne E Lindholm et al.   Epigenetics

PGC1-α over-expression prevents metabolic alterations and soleus muscle atrophy in hindlimb unloaded mice

(2014) Jessica Cannavino et al.   JOURNAL OF PHYSIOLOGY-LONDON

The many roles of PGC-1α in muscle — recent developments

(2014) Mun Chun Chan et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

BoxPlotR: a web tool for generation of box plots

(2014) Michaela Spitzer et al.   NATURE METHODS

NFATc1 Controls Skeletal Muscle Fiber Type and Is a Negative Regulator of MyoD Activity

(2014) Melissa L. Ehlers et al.   Cell Reports

Post-natal induction of PGC-1α protects against severe muscle dystrophy independently of utrophin

(2014) Mun Chan et al.   Skeletal Muscle

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

Exercise Metabolism and the Molecular Regulation of Skeletal Muscle Adaptation

(2013) Brendan Egan et al.   Cell Metabolism

Muscle ERRγ mitigates Duchenne muscular dystrophy via metabolic and angiogenic reprogramming

(2013) Antonios Matsakas et al.   FASEB JOURNAL

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

(2013) G. C. A. Taylor et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites

(2013) Yupeng Zheng et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Elevated PGC-1α Activity Sustains Mitochondrial Biogenesis and Muscle Function without Extending Survival in a Mouse Model of Inherited ALS

(2012) Sandrine Da Cruz et al.   Cell Metabolism

Revascularization of Ischemic Skeletal Muscle by Estrogen-Related Receptor-γ

(2012) Antonios Matsakas et al.   CIRCULATION RESEARCH

PGC-1α Improves Glucose Homeostasis in Skeletal Muscle in an Activity-Dependent Manner

(2012) Serge Summermatter et al.   DIABETES

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

(2012) R. Blum et al.   GENES & DEVELOPMENT

Increased mitochondrial biogenesis in muscle improves aging phenotypes in the mtDNA mutator mouse

(2012) Lloye M. Dillon et al.   HUMAN MOLECULAR GENETICS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Genesis of muscle fiber-type diversity during mouse embryogenesis relies on Six1 and Six4 gene expression

(2011) Anne-Françoise Richard et al.   DEVELOPMENTAL BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Fiber Types in Mammalian Skeletal Muscles

(2011) Stefano Schiaffino et al.   PHYSIOLOGICAL REVIEWS

Genome-wide remodeling of the epigenetic landscape during myogenic differentiation

(2011) P. Asp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Total Skeletal Muscle PGC-1 Deficiency Uncouples Mitochondrial Derangements from Fiber Type Determination and Insulin Sensitivity

(2010) Christoph Zechner et al.   Cell Metabolism

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

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

A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype

(2010) Pernille Keller et al.   JOURNAL OF APPLIED PHYSIOLOGY

Histone modifications and exercise adaptations

(2010) Sean L. McGee et al.   JOURNAL OF APPLIED PHYSIOLOGY

An Atypical E3 Ligase Zinc Finger Protein 91 Stabilizes and Activates NF-κB-inducing Kinase via Lys63-linked Ubiquitination

(2010) Xuejun Jin 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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

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

PGC-1α plays a functional role in exercise-induced mitochondrial biogenesis and angiogenesis but not fiber-type transformation in mouse skeletal muscle

(2009) Tuoyu Geng et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

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

(2009) Nathaniel D. Heintzman et al.   NATURE

The transcriptional coactivator PGC-1α mediates exercise-induced angiogenesis in skeletal muscle

(2009) Jessica Chinsomboon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Muscle-specific expression of PPARγ coactivator-1α improves exercise performance and increases peak oxygen uptake

(2008) Jennifer A. Calvo et al.   JOURNAL OF APPLIED PHYSIOLOGY

Overexpression of TEAD-1 in Transgenic Mouse Striated Muscles Produces a Slower Skeletal Muscle Contractile Phenotype

(2008) Richard W. Tsika et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HIF-independent regulation of VEGF and angiogenesis by the transcriptional coactivator PGC-1α

(2008) Zoltan Arany et al.   NATURE