Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability

TRITHORAX-dependent arginine methylation of HSP68 mediates circadian repression by PERIOD in the monarch butterfly

(2022) Ying Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals

(2022) Daniela Marzoll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states

(2021) Emily J. Collins et al.   GENOME RESEARCH

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

(2021) Lori B. Huberman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biochemical mechanisms of period control within the mammalian circadian clock

(2021) Jonathan M. Philpott et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A global search for novel transcription factors impacting theNeurospora crassacircadian clock

(2021) Felipe Muñoz-Guzmán et al.   G3-Genes Genomes Genetics

Vertebrate cell culture as an experimental approach – limitations and solutions

(2021) Mohammad Abbas et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

FRQ-CK1 Interaction Underlies Temperature Compensation of the Neurospora Circadian Clock

(2021) Yue Hu et al.   mBio

Synchronization between peripheral circadian clock and feeding-fasting cycles in microfluidic device sustains oscillatory pattern of transcriptome

(2021) Onelia Gagliano et al.   Nature Communications

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch

(2020) Jonathan M Philpott et al.   eLife

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

(2020) Yuchen Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Circadian clock control of eIF2α phosphorylation is necessary for rhythmic translation initiation

(2020) Shanta Karki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupled network of the circadian clocks: a driving force of rhythmic physiology

(2020) Anna‐Marie Finger et al.   FEBS LETTERS

Bayesian modeling reveals metabolite‐dependent ultrasensitivity in the cyanobacterial circadian clock

(2020) Lu Hong et al.   Molecular Systems Biology

PRD-2 directly regulates casein kinase I and counteracts nonsense-mediated decay in the Neurospora circadian clock

(2020) Christina M Kelliher et al.   eLife

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(2019) Jennifer J. Loros   EUROPEAN JOURNAL OF NEUROSCIENCE

The Phospho-Code Determining Circadian Feedback Loop Closure and Output in Neurospora

(2019) Bin Wang et al.   MOLECULAR CELL

Circadian clock regulation of the glycogen synthase (gsn) gene by WCC is critical for rhythmic glycogen metabolism in Neurospora crassa

(2019) Mokryun Baek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Inactivation Switch Enables Rhythms in a Neurospora Clock Model

(2019) Abhishek Upadhyay et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Evaluating the circadian rhythm and response to glucose addition in dispersed growth cultures of Neurospora crassa

(2019) Christina M. Kelliher et al.   Fungal Biology

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

mTOR signaling regulates central and peripheral circadian clock function

(2018) Chidambaram Ramanathan et al.   PLoS Genetics

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

(2018) Zhipeng Zhou et al.   eLife

ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

(2018) Vincent T Bicocca et al.   eLife

Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways

(2018) Jennifer M. Hurley et al.   Cell Systems

Up-Frameshift Protein UPF1 RegulatesNeurospora crassaCircadian and Diurnal Growth Rhythms

(2017) Yilan Wu et al.   GENETICS

The small G protein RAS2 is involved in the metabolic compensation of the circadian clock in the circadian modelNeurospora crassa

(2017) Norbert Gyöngyösi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock

(2017) Yuta Shinohara et al.   MOLECULAR CELL

Principles for circadian orchestration of metabolic pathways

(2017) Kevin Thurley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Up-Frameshift Protein UPF1 RegulatesNeurospora crassaCircadian and Diurnal Growth Rhythms

(2017) Yilan Wu et al.   GENETICS

Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa

(2016) Consuelo Olivares-Yañez et al.   GENETICS

Suppression of WHITE COLLAR-independentfrequencyTranscription by Histone H3 Lysine 36 Methyltransferase SET-2 Is Necessary for Clock Function inNeurospora

(2016) Guangyan Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa

(2016) Consuelo Olivares-Yañez et al.   GENETICS

Mathematical Modeling and Validation of Glucose Compensation of the Neurospora Circadian Clock

(2015) Andrey A. Dovzhenok et al.   BIOPHYSICAL JOURNAL

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

(2015) Gad Asher et al.   CELL

Circadian timing of metabolism in animal models and humans

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Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-IndependentfrequencyTranscription through Phosphorylation of RCM-1

(2015) Xiao Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of theNeurosporacircadian clock

(2015) Jillian M. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoupling circadian clock protein turnover from circadian period determination

(2015) L. F. Larrondo et al.   SCIENCE

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

(2015) Gregory J. Hogan et al.   PLOS BIOLOGY

Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora

(2015) Cigdem Sancar et al.   PLoS Genetics

Metabolic Compensation and Circadian Resilience in Prokaryotic Cyanobacteria

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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(2014) Gencer Sancar et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

CLOCK:BMAL1 is a pioneer-like transcription factor

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

Analysis of clock-regulated genes inNeurosporareveals widespread posttranscriptional control of metabolic potential

(2014) Jennifer M. Hurley 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

Compensation for intracellular environment in expression levels of mammalian circadian clock genes

(2014) Ritsuko Matsumura et al.   Scientific Reports

Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa

(2014) C. Wu et al.   G3-Genes Genomes Genetics

Cell Type-Specific Functions of Period Genes Revealed by Novel Adipocyte and Hepatocyte Circadian Clock Models

(2014) Chidambaram Ramanathan et al.   PLoS Genetics

Neurospora WC-1 Recruits SWI/SNF to Remodel frequency and Initiate a Circadian Cycle

(2014) Bin Wang et al.   PLoS Genetics

Methylation of Histone H3 on Lysine 4 by the Lysine Methyltransferase SET1 Protein Is Needed for Normal Clock Gene Expression

(2013) Hamidah Raduwan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Conserved RNA Helicase FRH Acts Nonenzymatically to Support the Intrinsically Disordered Neurospora Clock Protein FRQ

(2013) Jennifer M. Hurley et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Robust and tunable circadian rhythms from differentially sensitive catalytic domains

(2013) C. Phong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Suppression of WC-independent frequency transcription by RCO-1 is essential for Neurospora circadian clock

(2013) Z. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet

(2012) Megumi Hatori et al.   Cell Metabolism

High-resolution spatiotemporal analysis of gene expression in real time: In vivo analysis of circadian rhythms in Neurospora crassa using a FREQUENCY-luciferase translational reporter

(2012) Luis F. Larrondo et al.   FUNGAL GENETICS AND BIOLOGY

Metabolic compensation of the Neurospora clock by a glucose-dependent feedback of the circadian repressor CSP1 on the core oscillator

(2012) G. Sancar et al.   GENES & DEVELOPMENT

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

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

A Global Circadian Repressor Controls Antiphasic Expression of Metabolic Genes in Neurospora

(2011) Gencer Sancar et al.   MOLECULAR CELL

Transcription Factors in Light and Circadian Clock Signaling Networks Revealed by Genomewide Mapping of Direct Targets for Neurospora White Collar Complex

(2010) Kristina M. Smith et al.   EUKARYOTIC CELL

Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes

(2010) Biliana Marcheva et al.   NATURE

The histone methyltransferase MLL1 permits the oscillation of circadian gene expression

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

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

The Functional Interplay between Protein Kinase CK2 and CCA1 Transcriptional Activity Is Essential for Clock Temperature Compensation in Arabidopsis

(2010) Sergi Portolés et al.   PLoS Genetics

A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

(2009) Eric E. Zhang et al.   CELL

A Role for Casein Kinase 2 in the Mechanism Underlying Circadian Temperature Compensation

(2009) Arun Mehra et al.   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora

(2009) Chen-Hui Chen et al.   EMBO JOURNAL

A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock

(2009) B. Maier et al.   GENES & DEVELOPMENT

FRQ-Interacting RNA Helicase Mediates Negative and Positive Feedback in the Neurospora Circadian Clock

(2009) M. Shi et al.   GENETICS

A Phylogenetically Conserved DNA Damage Response Resets the Circadian Clock

(2009) Joshua J. Gamsby et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Network Features of the Mammalian Circadian Clock

(2009) Julie E Baggs et al.   PLOS BIOLOGY

WAVECLOCK: wavelet analysis of circadian oscillation

(2008) Tom S. Price et al.   BIOINFORMATICS

Circadian gene expression is resilient to large fluctuations in overall transcription rates

(2008) Charna Dibner et al.   EMBO JOURNAL

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

(2008) R. Lambreghts et al.   GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY