Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

(2019) Joshua R. Beytebiere et al.   GENES & DEVELOPMENT

Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression

(2019) Annaël Brunet et al.   Frontiers in Genetics

Clock-dependent chromatin topology modulates circadian transcription and behavior

(2018) Jérôme Mermet et al.   GENES & DEVELOPMENT

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

(2018) Jingkui Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Yong Hoon Kim et al.   SCIENCE

The interdependence of gene-regulatory elements and the 3D genome

(2018) Marit W. Vermunt et al.   JOURNAL OF CELL BIOLOGY

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior

(2018) Jake Yeung et al.   TRENDS IN GENETICS

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

(2017) Jake Yeung et al.   GENOME RESEARCH

What shapes eukaryotic transcriptional bursting?

(2017) Damien Nicolas et al.   Molecular BioSystems

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

(2017) Daniel Mauvoisin et al.   Cell Reports

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Lipidomics Analyses Reveal Temporal and Spatial Lipid Organization and Uncover Daily Oscillations in Intracellular Organelles

(2016) Rona Aviram et al.   MOLECULAR CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

(2016) Jérôme Mermet et al.   Cold Spring Harbor Perspectives in Biology

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

(2016) Yichi Xu et al.   PLoS Genetics

PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription

(2015) Honglei Zhao et al.   MOLECULAR CELL

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

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

(2014) Fabrice P. A. David et al.   PLoS One

Hepatocyte circadian clock controls acetaminophen bioactivation through NADPH-cytochrome P450 oxidoreductase

(2014) Brian P. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

(2013) Lorena Aguilar-Arnal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Circadian Clock NAD+ Cycle Drives Mitochondrial Oxidative Metabolism in Mice

(2013) C. B. Peek et al.   SCIENCE

Circadian regulation of low density lipoprotein receptor promoter activity by CLOCK/BMAL1, Hes1 and Hes6

(2012) Yeon-Ju Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

(2012) Tom Sexton et al.   Nature Protocols

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

(2012) N. Koike et al.   SCIENCE

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

The Mammalian Circadian Timing System: Organization and Coordination of Central and Peripheral Clocks

(2010) Charna Dibner et al.   Annual Review of Physiology

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Circadian Control of the NAD+ Salvage Pathway by CLOCK-SIRT1

(2009) Y. Nakahata et al.   SCIENCE

Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD+ Biosynthesis

(2009) K. M. Ramsey et al.   SCIENCE

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

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

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