Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle

(2018) Laurent Perrin et al.   eLife

Lipidomics reveals diurnal lipid oscillations in human skeletal muscle persisting in cellular myotubes cultured in vitro

(2017) Ursula Loizides-Mangold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rev-erb-α regulates atrophy-related genes to control skeletal muscle mass

(2017) Alicia Mayeuf-Louchart et al.   Scientific Reports

Bmal1 function in skeletal muscle regulates sleep

(2017) J Christopher Ehlen et al.   eLife

Rev-Erb co-regulates muscle regeneration via tethered interaction with the NF-Y cistrome

(2017) Ryan D. Welch et al.   Molecular Metabolism

Pharmacological inhibition of REV-ERB stimulates differentiation, inhibits turnover and reduces fibrosis in dystrophic muscle

(2017) Ryan D. Welch et al.   Scientific Reports

Coenzyme Q biosynthesis in health and disease

(2016) Manuel Jesús Acosta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion

(2016) Sungguan Hong et al.   NATURE MEDICINE

Perturbed rhythmic activation of signaling pathways in mice deficient for Sterol Carrier Protein 2-dependent diurnal lipid transport and metabolism

(2016) Céline Jouffe et al.   Scientific Reports

S6K1 Is Required for Increasing Skeletal Muscle Force during Hypertrophy

(2016) Manuela Marabita et al.   Cell Reports

Demonstration of a day-night rhythm in human skeletal muscle oxidative capacity

(2016) Dirk van Moorsel et al.   Molecular Metabolism

The functional significance of the skeletal muscle clock: lessons from Bmal1 knockout models

(2016) Stefano Schiaffino et al.   Skeletal Muscle

The beneficial role of proteolysis in skeletal muscle growth and stress adaptation

(2016) Ryan A. V. Bell et al.   Skeletal Muscle

Muscle-specific loss of Bmal1 leads to disrupted tissue glucose metabolism and systemic glucose homeostasis

(2016) Brianna D. Harfmann et al.   Skeletal Muscle

Synchronized human skeletal myotubes of lean, obese and type 2 diabetic patients maintain circadian oscillation of clock genes

(2016) Jan Hansen et al.   Scientific Reports

The Circadian Protein BMAL1 Regulates Translation in Response to S6K1-Mediated Phosphorylation

(2015) Jonathan O. Lipton et al.   CELL

The molecular clock as a metabolic rheostat

(2015) M. Perelis et al.   DIABETES OBESITY & METABOLISM

Ascribing novel functions to the sarcomeric protein, myosin binding protein H (MyBPH) in cardiac sarcomere contraction

(2015) Jomien Mouton et al.   EXPERIMENTAL CELL RESEARCH

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver

(2015) Serena Abbondante et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

Discrete functions of nuclear receptor Rev-erb  couple metabolism to the clock

(2015) Y. Zhang et al.   SCIENCE

Exercise Pills: At the Starting Line

(2015) Shunchang Li et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

A muscle-liver-fat signalling axis is essential for central control of adaptive adipose remodelling

(2015) Noriaki Shimizu et al.   Nature Communications

Human skeletal myotubes display a cell-autonomous circadian clock implicated in basal myokine secretion

(2015) Laurent Perrin et al.   Molecular Metabolism

The calcineurin-NFAT pathway controls activity-dependent circadian gene expression in slow skeletal muscle

(2015) Kenneth A. Dyar et al.   Molecular Metabolism

The endogenous molecular clock orchestrates the temporal separation of substrate metabolism in skeletal muscle

(2015) Brian A Hodge et al.   Skeletal Muscle

The Therapeutic Potential of Nuclear Receptor Modulators for Treatment of Metabolic Disorders: PPARγ, RORs, and Rev-erbs

(2014) David P. Marciano et al.   Cell Metabolism

A versatile ultra-high performance LC-MS method for lipid profiling

(2014) Oskar L. Knittelfelder et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Metabolomics reveal 1-palmitoyl lysophosphatidylcholine production by peroxisome proliferator-activated receptor α

(2014) Haruya Takahashi et al.   JOURNAL OF LIPID RESEARCH

An atlas of genetic influences on human blood metabolites

(2014) So-Youn Shin et al.   NATURE GENETICS

REV-ERB and ROR nuclear receptors as drug targets

(2014) Douglas J. Kojetin et al.   NATURE REVIEWS DRUG DISCOVERY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Overexpression of PLIN5 in skeletal muscle promotes oxidative gene expression and intramyocellular lipid content without compromising insulin sensitivity

(2013) M. Bosma et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Chronic rapamycin treatment or lack ofS6K1does not reduce ribosome activity in vivo

(2013) Michael G Garelick et al.   CELL CYCLE

Mechanisms regulating skeletal muscle growth and atrophy

(2013) Stefano Schiaffino et al.   FEBS Journal

Endurance training ameliorates the metabolic and performance characteristics of circadian Clock mutant mice

(2013) Stephen Pastore et al.   JOURNAL OF APPLIED PHYSIOLOGY

Fatty acids regulate perilipin5 in muscle by activating PPARδ

(2013) Christian Bindesbøll et al.   JOURNAL OF LIPID RESEARCH

Rev-erb-α modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy

(2013) Estelle Woldt et al.   NATURE MEDICINE

Metabolism and the Circadian Clock Converge

(2013) Kristin Eckel-Mahan et al.   PHYSIOLOGICAL REVIEWS

Measuring Energy Metabolism in the Mouse – Theoretical, Practical, and Analytical Considerations

(2013) John R. Speakman   Frontiers in Physiology

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

(2013) Kenneth A. Dyar et al.   Molecular Metabolism

Lipid-Induced Mitochondrial Stress and Insulin Action in Muscle

(2012) Deborah M. Muoio et al.   Cell Metabolism

Adiponutrin Functions as a Nutritionally Regulated Lysophosphatidic Acid Acyltransferase

(2012) Manju Kumari et al.   Cell Metabolism

Interplay between Lipids and Branched-Chain Amino Acids in Development of Insulin Resistance

(2012) Christopher B. Newgard   Cell Metabolism

Rev-erb  and Rev-erb  coordinately protect the circadian clock and normal metabolic function

(2012) A. Bugge et al.   GENES & DEVELOPMENT

Proteasome-dependent Activation of Mammalian Target of Rapamycin Complex 1 (mTORC1) Is Essential for Autophagy Suppression and Muscle Remodeling Following Denervation

(2012) Pham Nguyen Quy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β

(2012) Han Cho et al.   NATURE

Assessment of mitochondrial respiratory chain enzymatic activities on tissues and cultured cells

(2012) Marco Spinazzi et al.   Nature Protocols

Coordination of the transcriptome and metabolome by the circadian clock

(2012) K. L. Eckel-Mahan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex

(2012) N. Huang et al.   SCIENCE

Linking mitochondrial bioenergetics to insulin resistance via redox biology

(2012) Kelsey H. Fisher-Wellman et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

PPARs are a unique set of fatty acid regulated transcription factors controlling both lipid metabolism and inflammation

(2011) Tamas Varga et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

A guide to analysis of mouse energy metabolism

(2011) Matthias H Tschöp et al.   NATURE METHODS

Direct Regulation of CLOCK Expression by REV-ERB

(2011) Christine Crumbley et al.   PLoS One

Proline- and acidic amino acid-rich basic leucine zipper proteins modulate peroxisome proliferator-activated receptor   (PPAR ) activity

(2011) F. Gachon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

(2011) D. Feng et al.   SCIENCE

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Identification of SR8278, a Synthetic Antagonist of the Nuclear Heme Receptor REV-ERB

(2010) Douglas Kojetin et al.   ACS Chemical Biology

Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data

(2010) Jürgen Hartler et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Mitochondrial fission and remodelling contributes to muscle atrophy

(2010) Vanina Romanello et al.   EMBO JOURNAL

Novel insights into the regulation of skeletal muscle protein synthesis as revealed by a new nonradioactive in vivo technique

(2010) Craig A. Goodman et al.   FASEB JOURNAL

Nonshivering thermogenesis and its adequate measurement in metabolic studies

(2010) B. Cannon et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria

(2010) Sneha S. Prasad et al.   JOURNAL OF LIPID RESEARCH

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The hypothalamic clock and its control of glucose homeostasis

(2010) Andries Kalsbeek et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Amino acid transceptors: gate keepers of nutrient exchange and regulators of nutrient signaling

(2009) Harinder S. Hundal et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Skeletal Muscle Insulin Resistance Is the Primary Defect in Type 2 Diabetes

(2009) R. A. DeFronzo et al.   DIABETES CARE

Inducible activation of Akt increases skeletal muscle mass and force without satellite cell activation

(2009) Bert Blaauw et al.   FASEB JOURNAL

Gold standards for scientists who are conducting animal-based exercise studies

(2009) Frank W. Booth et al.   JOURNAL OF APPLIED PHYSIOLOGY

PPARs and the orchestration of metabolic fuel selection

(2009) Mary C. Sugden et al.   PHARMACOLOGICAL RESEARCH

The glucocorticoid receptor and FOXO1 synergistically activate the skeletal muscle atrophy-associated MuRF1 gene

(2008) David S. Waddell et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

AMPK and PPARδ Agonists Are Exercise Mimetics

(2008) Vihang A. Narkar et al.   CELL

Metabolic profiling of PPARα−/− mice reveals defects in carnitine and amino acid homeostasis that are partially reversed by oral carnitine supplementation

(2008) Liza Makowski et al.   FASEB JOURNAL

Regulation of fatty acid uptake into tissues: lipoprotein lipase- and CD36-mediated pathways: Fig. 1.

(2008) Ira J. Goldberg et al.   JOURNAL OF LIPID RESEARCH

Thematic Review Series: Glycerolipids.DGAT enzymes and triacylglycerol biosynthesis

(2008) Chi-Liang Eric Yen et al.   JOURNAL OF LIPID RESEARCH

Whey Protein Ingestion Enhances Postprandial Anabolism during Short-Term Bed Rest in Young Men

(2008) Raffaella Antonione et al.   JOURNAL OF NUTRITION

Diet-induced obesity alters protein synthesis: tissue-specific effects in fasted versus fed mice

(2008) Stephanie R. Anderson et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Increased substrate oxidation and mitochondrial uncoupling in skeletal muscle of endurance-trained individuals

(2008) D. E. Befroy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY