Transcriptional architecture of the mammalian circadian clock

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Increased Melatonin Signaling Is a Risk Factor for Type 2 Diabetes

(2016) Tiinamaija Tuomi et al.   Cell Metabolism

The Difficult Journey from Genome-wide Association Studies to Pathophysiology: The Melatonin Receptor 1B (MT2) Paradigm

(2016) Amélie Bonnefond et al.   Cell Metabolism

Circadian Rhythm Disruption Promotes Lung Tumorigenesis

(2016) Thales Papagiannakopoulos et al.   Cell Metabolism

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Post-transcriptional control of the mammalian circadian clock: implications for health and disease

(2016) Marco Preußner et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner

(2016) Yi-Ying Chiou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person

(2016) Youna Hu et al.   Nature Communications

Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank

(2016) Jacqueline M. Lane et al.   Nature Communications

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

(2016) Yichi Xu et al.   PLoS Genetics

Genome-Wide Association Analyses in 128,266 Individuals Identifies New Morningness and Sleep Duration Loci

(2016) Samuel E. Jones et al.   PLoS Genetics

Giving Time Purpose: TheSynechococcus elongatusClock in a Broader Network Context

(2015) Ryan K. Shultzaberger et al.   Annual Review of Genetics

Time for Food: The Intimate Interplay between Nutrition, Metabolism, and the Circadian Clock

(2015) Gad Asher et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Circadian clocks, epigenetics, and cancer

(2015) Selma Masri et al.   CURRENT OPINION IN ONCOLOGY

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

(2015) Thomas Cremer et al.   FEBS LETTERS

Ribosome profiling reveals an important role for translational control in circadian gene expression

(2015) Christopher Jang et al.   GENOME RESEARCH

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

(2015) Peggy Janich et al.   GENOME RESEARCH

A Period2 Phosphoswitch Regulates and Temperature Compensates Circadian Period

(2015) Min Zhou et al.   MOLECULAR CELL

Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude via REV-ERB Loading

(2015) Bokai Zhu et al.   MOLECULAR CELL

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

(2015) Honglei Zhao et al.   MOLECULAR CELL

Structural integration in hypoxia-inducible factors

(2015) Dalei Wu et al.   NATURE

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Integrating circadian dynamics with physiological processes in plants

(2015) Kathleen Greenham et al.   NATURE REVIEWS GENETICS

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone monoubiquitination by Clock–Bmal1 complex marks Per1 and Per2 genes for circadian feedback

(2015) Alfred G Tamayo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NAD+-SIRT1 control of H3K4 trimethylation through circadian deacetylation of MLL1

(2015) Lorena Aguilar-Arnal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Functional organization of the human 4D Nucleome

(2015) Haiming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pancreatic   cell enhancers regulate rhythmic transcription of genes controlling insulin secretion

(2015) M. Perelis et al.   SCIENCE

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

(2015) Y. Zhang et al.   SCIENCE

A tunable artificial circadian clock in clock-defective mice

(2015) Matthew D’Alessandro et al.   Nature Communications

Histone monoubiquitination by Clock–Bmal1 complex marks Per1 and Per2 genes for circadian feedback

(2015) Alfred G Tamayo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NAD+-SIRT1 control of H3K4 trimethylation through circadian deacetylation of MLL1

(2015) Lorena Aguilar-Arnal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale

(2015) Guang-Zhong Wang et al.   Cell Reports

Metabolic Compensation and Circadian Resilience in Prokaryotic Cyanobacteria

(2014) Carl Hirschie Johnson et al.   Annual Review of Biochemistry

Interactive Features of Proteins Composing Eukaryotic Circadian Clocks

(2014) Brian R. Crane et al.   Annual Review of Biochemistry

Metabolic and Nontranscriptional Circadian Clocks: Eukaryotes

(2014) Akhilesh B. Reddy et al.   Annual Review of Biochemistry

Circadian Genomics Reveal a Role for Post-transcriptional Regulation in Mammals

(2014) Shihoko Kojima et al.   BIOCHEMISTRY

Circadian Clock, Cancer, and Chemotherapy

(2014) Aziz Sancar et al.   BIOCHEMISTRY

Mechanism of the Neurospora Circadian Clock, a FREQUENCY-centric View

(2014) Joonseok Cha et al.   BIOCHEMISTRY

Emerging Models for the Molecular Basis of Mammalian Circadian Timing

(2014) Chelsea L. Gustafson et al.   BIOCHEMISTRY

Interaction of Circadian Clock Proteins CRY1 and PER2 Is Modulated by Zinc Binding and Disulfide Bond Formation

(2014) Ira Schmalen et al.   CELL

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

CLOCK:BMAL1 is a pioneer-like transcription factor

(2014) J. S. Menet et al.   GENES & DEVELOPMENT

Dual modes of CLOCK:BMAL1 inhibition mediated by Cryptochrome and Period proteins in the mammalian circadian clock

(2014) Rui Ye et al.   GENES & DEVELOPMENT

Circadian Clock Proteins and Immunity

(2014) Anne M. Curtis et al.   IMMUNITY

Gene Model 129 (Gm129) Encodes a Novel Transcriptional Repressor That Modulates Circadian Gene Expression

(2014) Yunus Annayev et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CLOCK-Controlled Polyphonic Regulation of Circadian Rhythms through Canonical and Noncanonical E-Boxes

(2014) H. Yoshitane et al.   MOLECULAR AND CELLULAR BIOLOGY

Specificity in Circadian Clock Feedback from Targeted Reconstitution of the NuRD Corepressor

(2014) Jin Young Kim et al.   MOLECULAR CELL

Phosphorylation of LSD1 by PKCα Is Crucial for Circadian Rhythmicity and Phase Resetting

(2014) Hye Jin Nam et al.   MOLECULAR CELL

Rhythmic U2af26 Alternative Splicing Controls PERIOD1 Stability and the Circadian Clock in Mice

(2014) Marco Preußner et al.   MOLECULAR CELL

Novel loci associated with usual sleep duration: the CHARGE Consortium Genome-Wide Association Study

(2014) D J Gottlieb et al.   MOLECULAR PSYCHIATRY

Light as a central modulator of circadian rhythms, sleep and affect

(2014) Tara A. LeGates et al.   NATURE REVIEWS NEUROSCIENCE

Temporal orchestration of repressive chromatin modifiers by circadian clock Period complexes

(2014) Hao A Duong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin landscape and circadian dynamics: Spatial and temporal organization of clock transcription

(2014) Lorena Aguilar-Arnal 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

SRC-2 Is an Essential Coactivator for Orchestrating Metabolism and Circadian Rhythm

(2014) Erin Stashi et al.   Cell Reports

Machine Learning Helps Identify CHRONO as a Circadian Clock Component

(2014) Ron C. Anafi et al.   PLOS BIOLOGY

A Novel Protein, CHRONO, Functions as a Core Component of the Mammalian Circadian Clock

(2014) Akihiro Goriki et al.   PLOS BIOLOGY

Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex

(2014) Shannon N Nangle et al.   eLife

Structures of Drosophila Cryptochrome and Mouse Cryptochrome1 Provide Insight into Circadian Function

(2013) Anna Czarna et al.   CELL

Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm

(2013) Seung-Hee Yoo et al.   CELL

FBXL21 Regulates Oscillation of the Circadian Clock through Ubiquitination and Stabilization of Cryptochromes

(2013) Arisa Hirano et al.   CELL

Blood-Borne Circadian Signal Stimulates Daily Oscillations in Actin Dynamics and SRF Activity

(2013) Alan Gerber et al.   CELL

Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

(2013) Shannon Nangle et al.   CELL RESEARCH

SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket

(2013) Weiman Xing et al.   NATURE

Emerging roles for post-transcriptional regulation in circadian clocks

(2013) Chunghun Lim et al.   NATURE NEUROSCIENCE

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

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

Metabolism and the Circadian Clock Converge

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

Histone methyltransferase MLL3 contributes to genome-scale circadian transcription

(2013) Utham K. Valekunja et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A positive feedback loop links circadian clock factor CLOCK-BMAL1 to the basic transcriptional machinery

(2013) L. Lande-Diner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Gene Bmal1 Regulates Diurnal Oscillations of Ly6Chi Inflammatory Monocytes

(2013) K. D. Nguyen et al.   SCIENCE

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice

(2013) Kazuhiro Shimomura et al.   eLife

Central and Peripheral Circadian Clocks in Mammals

(2012) Jennifer A. Mohawk et al.   Annual Review of Neuroscience

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

(2012) Christopher Vollmers et al.   Cell Metabolism

Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA

(2012) Zixi Wang et al.   CELL RESEARCH

Genetic basis of human circadian rhythm disorders

(2012) Christopher R. Jones et al.   EXPERIMENTAL NEUROLOGY

Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

(2012) S. Kojima et al.   GENES & DEVELOPMENT

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

(2012) Markus Stratmann et al.   MOLECULAR CELL

Clocks, Metabolism, and the Epigenome

(2012) Dan Feng et al.   MOLECULAR CELL

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

(2012) Han Cho et al.   NATURE

Circadian topology of metabolism

(2012) Joseph Bass   NATURE

Rare MTNR1B variants impairing melatonin receptor 1B function contribute to type 2 diabetes

(2012) Amélie Bonnefond et al.   NATURE GENETICS

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Timing to Perfection: The Biology of Central and Peripheral Circadian Clocks

(2012) Urs Albrecht   NEURON

Unwinding the differences of the mammalian PERIOD clock proteins from crystal structure to cellular function

(2012) N. Kucera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Small Molecule Activators of Cryptochrome

(2012) T. Hirota et al.   SCIENCE

Feedback Regulation of Transcriptional Termination by the Mammalian Circadian Clock PERIOD Complex

(2012) K. Padmanabhan et al.   SCIENCE

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

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

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function

(2011) Maki Ukai-Tadenuma et al.   CELL

Biochemical Analysis of the Canonical Model for the Mammalian Circadian Clock

(2011) Rui Ye et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stoichiometric Relationship among Clock Proteins Determines Robustness of Circadian Rhythms

(2011) Yongjin Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tuning the Period of the Mammalian Circadian Clock: Additive and Independent Effects of CK1 Tau and Fbxl3Afh Mutations on Mouse Circadian Behavior and Molecular Pacemaking

(2011) E. S. Maywood et al.   JOURNAL OF NEUROSCIENCE

Melatonin: Both master clock output and internal time-giver in the circadian clocks network

(2011) Paul Pevet et al.   JOURNAL OF PHYSIOLOGY-PARIS

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

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

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The period of the circadian oscillator is primarily determined by the balance between casein kinase 1 and protein phosphatase 1

(2011) H.-m. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Lysine Demethylase JARID1a Activates CLOCK-BMAL1 and Influences the Circadian Clock

(2011) L. DiTacchio et al.   SCIENCE

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

(2011) D. Feng et al.   SCIENCE

A Molecular Mechanism for Circadian Clock Negative Feedback

(2011) H. A. Duong et al.   SCIENCE

Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus

(2011) Masao Doi et al.   Nature Communications

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Circadian Control of Global Gene Expression Patterns

(2010) Colleen J. Doherty et al.   Annual Review of Genetics

Circadian Organization of Behavior and Physiology in Drosophila

(2010) Ravi Allada et al.   Annual Review of Physiology

Suprachiasmatic Nucleus: Cell Autonomy and Network Properties

(2010) David K. Welsh et al.   Annual Review of Physiology

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

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

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA

(2010) J. S. Menet et al.   GENES & DEVELOPMENT

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

(2010) Josée Dupuis et al.   NATURE GENETICS

The histone methyltransferase MLL1 permits the oscillation of circadian gene expression

(2010) Sayako Katada et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Casein Kinase 1 Delta Regulates the Pace of the Mammalian Circadian Clock

(2009) J.-P. Etchegaray et al.   MOLECULAR AND CELLULAR BIOLOGY

Rhythmic PER Abundance Defines a Critical Nodal Point for Negative Feedback within the Circadian Clock Mechanism

(2009) Rongmin Chen et al.   MOLECULAR CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

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

(2009) Y. Nakahata et al.   SCIENCE

AMPK Regulates the Circadian Clock by Cryptochrome Phosphorylation and Degradation

(2009) K. A. Lamia et al.   SCIENCE

Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD+ Biosynthesis

(2009) K. M. Ramsey et al.   SCIENCE

CBP/p300 is a cell type-specific modulator of CLOCK/BMAL1-mediated transcription

(2009) Hiroshi Hosoda et al.   Molecular Brain

Structural and Functional Analyses of PAS Domain Interactions of the Clock Proteins Drosophila PERIOD and Mouse PERIOD2

(2009) Sven Hennig et al.   PLOS BIOLOGY

The Implications of Multiple Circadian Clock Origins

(2009) Michael Rosbash   PLOS BIOLOGY

Harmonics of Circadian Gene Transcription in Mammals

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

The NAD+-Dependent Deacetylase SIRT1 Modulates CLOCK-Mediated Chromatin Remodeling and Circadian Control

(2008) Yasukazu Nakahata et al.   CELL

SIRT1 Regulates Circadian Clock Gene Expression through PER2 Deacetylation

(2008) Gad Asher et al.   CELL

Dual Modification of BMAL1 by SUMO2/3 and Ubiquitin Promotes Circadian Activation of the CLOCK/BMAL1 Complex

(2008) J. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

Common variant in MTNR1B associated with increased risk of type 2 diabetes and impaired early insulin secretion

(2008) Valeriya Lyssenko et al.   NATURE GENETICS

Variants in MTNR1B influence fasting glucose levels

(2008) Inga Prokopenko et al.   NATURE GENETICS

A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk

(2008) Nabila Bouatia-Naji et al.   NATURE GENETICS

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

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

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Setting Clock Speed in Mammals: The CK1ɛ tau Mutation in Mice Accelerates Circadian Pacemakers by Selectively Destabilizing PERIOD Proteins

(2008) Qing-Jun Meng et al.   NEURON

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE