Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Reciprocal localization of transcription factors YY1 and CP2c in spermatogonial stem cells and their putative roles during spermatogenesis

(2016) Ji Sook Kim et al.   ACTA HISTOCHEMICA

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein geneCirbp

(2016) Ivana Gotic et al.   GENES & DEVELOPMENT

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Circadian time signatures of fitness and disease

(2016) Joseph Bass et al.   SCIENCE

Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression

(2016) Yichi Xu et al.   PLoS Genetics

The Constitutive Activation of Egr-1/C/EBPa Mediates the Development of Type 2 Diabetes Mellitus by Enhancing Hepatic Gluconeogenesis

(2015) Ning Shen et al.   AMERICAN JOURNAL OF PATHOLOGY

Mining for novel candidate clock genes in the circadian regulatory network

(2015) Anuprabha Bhargava et al.   BMC Systems Biology

Circadian timing of metabolism in animal models and humans

(2015) C. Dibner et al.   JOURNAL OF INTERNAL MEDICINE

Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes

(2015) J. W. Lee et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver

(2015) Tara L. Conforto et al.   MOLECULAR ENDOCRINOLOGY

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

(2015) Florian Atger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Y. Zhang et al.   SCIENCE

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

MACE: model based analysis of ChIP-exo

(2014) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data

(2013) Anastasia Deckard et al.   BIOINFORMATICS

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

Hepatic glucose sensing and integrative pathways in the liver

(2013) Maaike H. Oosterveer et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Glucagon regulates gluconeogenesis through KAT2B- and WDR5-mediated epigenetic effects

(2013) Kim Ravnskjaer et al.   JOURNAL OF CLINICAL INVESTIGATION

Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program

(2013) C Chauvin et al.   ONCOGENE

The Circadian Clock Coordinates Ribosome Biogenesis

(2013) Céline Jouffe et al.   PLOS BIOLOGY

Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome

(2012) Christopher Vollmers et al.   Cell Metabolism

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

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

The Circadian Clock Modulates Renal Sodium Handling

(2012) S. Nikolaeva et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

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

(2012) Han Cho et al.   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

(2012) J. Morf et al.   SCIENCE

Brain-Specific Rescue of Clock Reveals System-Driven Transcriptional Rhythms in Peripheral Tissue

(2012) Michael E. Hughes et al.   PLoS Genetics

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Disruption of the allosteric phosphorylase a regulation of the hepatic glycogen-targeted protein phosphatase 1 improves glucose tolerance in vivo

(2009) Ian R. Kelsall et al.   CELLULAR SIGNALLING

Regulation of Clock-Controlled Genes in Mammals

(2009) Katarzyna Bozek et al.   PLoS One

The key roles of elongases and desaturases in mammalian fatty acid metabolism: Insights from transgenic mice

(2009) Hervé Guillou et al.   PROGRESS IN LIPID RESEARCH

REV-ERBα Participates in Circadian SREBP Signaling and Bile Acid Homeostasis

(2009) Gwendal Le Martelot et al.   PLOS BIOLOGY

Harmonics of Circadian Gene Transcription in Mammals

(2009) Michael E. Hughes et al.   PLoS Genetics

Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor

(2008) H. Reinke et al.   GENES & DEVELOPMENT

Mixtures ofgPriors for Bayesian Variable Selection

(2008) Feng Liang et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The genetics of mammalian circadian order and disorder: implications for physiology and disease

(2008) Joseph S. Takahashi et al.   NATURE REVIEWS GENETICS

Physiological significance of a peripheral tissue circadian clock

(2008) K. A. Lamia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA