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

The Sequence Alignment/Map format and SAMtools

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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

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The Human Genome Browser at UCSC

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High-Resolution Profiling of Histone Methylations in the Human Genome

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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The Role of Chromatin during Transcription

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

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The emerging roles of m6A modification in liver carcinogenesis

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Decoupling PER phosphorylation, stability and rhythmic expression from circadian clock function by abolishing PER-CK1 interaction

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Regulated DNA Methylation and the Circadian Clock: Implications in Cancer

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Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock

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Oscillating primary transcripts harbor miRNAs with circadian functions

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Non-transcriptional processes in circadian rhythm generation

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Metabolic Implications of Circadian–HIF Crosstalk

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Common Functions of Disordered Proteins across Evolutionary Distant Organisms

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Revealing the hidden reality of the mammalian 12-h ultradian rhythms

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Evolution of mouse circadian enhancers from transposable elements

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

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Circadian events in human diseases and in cytochrome P450‐related drug metabolism and therapy

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The circadian system as an organizer of metabolism

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Photoperiodism dynamics during the domestication and improvement of soybean

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Emerging roles for microRNA in the regulation of Drosophila circadian clock

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Non-coding cis-element of Period2 is essential for maintaining organismal circadian behaviour and body temperature rhythmicity

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Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis

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Coordinate Regulation of Cholesterol and Bile Acid Metabolism by the Clock Modifier Nobiletin in Metabolically Challenged Old Mice

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Nonalcoholic fatty liver disease in CLOCK mutant mice

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The beneficial effects of intermittent fasting: an update on mechanism, and the role of circadian rhythm and gut microbiota

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CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy

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Histone Modification Patterns and Their Responses to Environment

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Chromatin remodeling and alternative splicing: Pre- and post-transcriptional regulation of the Arabidopsis circadian clock

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Manipulating the Circadian and Sleep Cycles to Protect Against Metabolic Disease

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Combined Pharmacological and Genetic Manipulations Unlock Unprecedented Temporal Elasticity and Reveal Phase-Specific Modulation of the Molecular Circadian Clock of the Mouse Suprachiasmatic Nucleus

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Circadian processes in the RNA life cycle

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Neuronal PAS domain 2 (Npas2) facilitated osseointegration of titanium implant with rough surface through a neuroskeletal mechanism

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Understanding m6A Function Through Uncovering the Diversity Roles of YTH Domain-Containing Proteins

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Circadian gene PER1 senses progesterone signal during human endometrial decidualization

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MRG15 orchestrates rhythmic epigenomic remodelling and controls hepatic lipid metabolism

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Assembly of a Comprehensive Regulatory Network for the Mammalian Circadian Clock: A Bioinformatics Approach

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The role of the circadian timing system on drug metabolism and detoxification: an update

Okyar, A., Civelek, D. Ö., Akyel, Y. K., Sürme, S., Kara, Z. P., & Kavaklı, İ. H. (2024) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1080/17425255.2024.2356167 · Cited by 39

RNA around the clock – regulation at the RNA level in biological timing

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Sexual Dimorphism in Circadian Physiology Is Altered in LXRα Deficient Mice

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Dual attenuation of proteasomal and autophagic BMAL1 degradation in ClockΔ19/+ mice contributes to improved glucose homeostasis

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Role of circadian gene Clock during differentiation of mouse pluripotent stem cells

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Inhibition of p38 MAPK activity leads to cell type-specific effects on the molecular circadian clock and time-dependent reduction of glioma cell invasiveness

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Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle

Szabó, Á., Papin, C., Cornu, D., Chélot, E., Lipinszki, Z., Udvardy, A., Redeker, V., Mayor, U., & Rouyer, F. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.04.064 · Cited by 39

An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals

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Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock

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Circadian regulation of gene expression: at the crossroads of transcriptional and post-transcriptional regulatory networks

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c-MYC targets the central oscillator gene Per1 and is regulated by the circadian clock at the post-transcriptional level

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Response of Peripheral Rhythms to the Timing of Food Intake

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Cell-Type-Specific Regulation of Nucleus Accumbens Synaptic Plasticity and Cocaine Reward Sensitivity by the Circadian Protein, NPAS2

Parekh, P. K., Logan, R. W., Ketchesin, K. D., Becker‐Krail, D. D., Shelton, M. A., Hildebrand, M. A., Barko, K., Huang, Y. H., & McClung, C. A. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.2233-18.2019 · Cited by 42

Circadian rhythms and proteomics: It's all about posttranslational modifications!

Mauvoisin, D. (2019) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1450 · Cited by 40

Transcription-based circadian mechanism controls the duration of molecular clock states in response to signaling inputs

Almeida, S., Madalena Chaves, A., & Delaunay, F. (2019) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2019.110015 · Cited by 37

The circadian clock gene Bmal1 facilitates cisplatin-induced renal injury and hepatization

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Heart neurons use clock genes to control myocyte proliferation

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Daily running enhances molecular and physiological circadian rhythms in skeletal muscle

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Circadian regulated control of myocardial ischemia-reperfusion injury

Rabinovich-Nikitin, I., & Kirshenbaum, L. A. (2022) · Trends in Cardiovascular Medicine · doi:10.1016/j.tcm.2022.09.003 · Cited by 38

Ageing and Low-Level Chronic Inflammation: The Role of the Biological Clock

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The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila

Kwok, R. S., Li, Y. H., Lei, A. J., Edery, I., & Chiu, J. C. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005307 · Cited by 37

Genetics of circadian rhythms

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Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health

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The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Furlan-Magaril, M., Ando-Kuri, M., Arzate-Mejía, R. G., Morf, J., Cairns, J., Román-Figueroa, A., Tenorio-Hernández, L., Poot-Hernández, A. C., Andrews, S., Várnai, C., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02374-3 · Cited by 39

Role of Melatonin in Cancer: Effect on Clock Genes

Rodríguez-Santana, C., Florido, J., Martínez-Ruiz, L., López‐Rodríguez, A., Acuña-Castroviejo, D., & Escames, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24031919 · Cited by 42

Rhythmic control of mRNA stability modulates circadian amplitude of mouse Period3 mRNA

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Day and night variations in the repair of ionizing-radiation-induced DNA damage in mouse splenocytes

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Ammonia-lowering activities and carbamoyl phosphate synthetase 1 (Cps1) induction mechanism of a natural flavonoid

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CLOCKWORK ORANGE Enhances PERIOD Mediated Rhythms in Transcriptional Repression by Antagonizing E-box Binding by CLOCK-CYCLE

Zhou, J., Yu, W., & Hardin, P. E. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006430 · Cited by 37

PER2 regulation of mammary gland development

McQueen, C. M., Schmitt, E. E., Sarkar, T. R., Epps, J. L., Metz, R. P., Earnest, D. J., Rijnkels, M., & Porter, W. W. (2018) · Development · doi:10.1242/dev.157966 · Cited by 36

MECHANISMS IN ENDOCRINOLOGY: A sense of time of the glucocorticoid circadian clock: from the ontogeny to the diagnosis of Cushing’s syndrome

Moreira, A. C., Antonini, S. R. R., & de Castro, M. (2018) · European Journal of Endocrinology · doi:10.1530/eje-18-0102 · Cited by 38

Systems Level Understanding of Circadian Integration with Cell Physiology

Morris, A. R., Stanton, D., Roman, D., & Liu, A. C. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.02.002 · Cited by 36

Clocks, Viruses, and Immunity: Lessons for the COVID-19 Pandemic

Sengupta, S., Ince, L. M., Sartor, F., Borrmann, H., Zhuang, X., Naik, A. S., Curtis, A. M., & McKeating, J. A. (2021) · Journal of Biological Rhythms · doi:10.1177/0748730420987669 · Cited by 36

CRY2 missense mutations suppress P53 and enhance cell growth

Chan, A. B., Parico, G. C. G., Fribourgh, J. L., Ibrahim, L. H., Bollong, M. J., Partch, C. L., & Lamia, K. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101416118 · Cited by 41

Clock-modified mesenchymal stromal cells therapy rescues molecular circadian oscillation and age-related bone loss via miR142-3p/Bmal1/YAP signaling axis

Cha, S., Wang, J., Lee, S. M., Tan, Z., Zhao, Q. S., & Bai, D. (2022) · Cell Death Discovery · doi:10.1038/s41420-022-00908-7 · Cited by 37

Shiftwork and Light at Night Negatively Impact Molecular and Endocrine Timekeeping in the Female Reproductive Axis in Humans and Rodents

Yaw, A. M., McLane-Svoboda, A. K., & Hoffmann, H. M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms22010324 · Cited by 44

Brain–body communication in metabolic control

Furlan, A., & Petrus, P. (2023) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2023.08.014 · Cited by 34

Epigenetic mechanisms in diurnal cycles of metabolism and neurodevelopment

Powell, W. T., & LaSalle, J. M. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv234 · Cited by 36

CATP is a critical component of the Neurospora circadian clock by regulating the nucleosome occupancy rhythm at the frequency locus

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Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase Nocturnin

Kojima, S., Gendreau, K. L., Sher-Chen, E. L., Gao, P., & Green, C. B. (2015) · Scientific Reports · doi:10.1038/srep17059 · Cited by 37

Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function

Shi, G., Xie, P., Qu, Z., Zhang, Z., Dong, Z., An, Y., Xing, L., Liu, Z., Dong, Y., Xu, G., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.076 · Cited by 37

The Liver Circadian Clock Modulates Biochemical and Physiological Responses to Metformin

Henriksson, E., Huber, A., Soto, E., Kriebs, A., Vaughan, M. E., Duglan, D., Chan, A. B., Papp, S. J., Nguyen, M., Afetian, M. E., et al. (2017) · Journal of Biological Rhythms · doi:10.1177/0748730417710348 · Cited by 37

Differential roles for cryptochromes in the mammalian retinal clock

Wong, J. C. Y., Smyllie, N. J., Banks, G. T., Pothecary, C. A., Barnard, A. R., Maywood, E. S., Jagannath, A., Hughes, S., van der Horst, G. T. J., MacLaren, R. E., et al. (2018) · The FASEB Journal · doi:10.1096/fj.201701165rr · Cited by 36

Post-translational Modifications are Required for Circadian Clock Regulation in Vertebrates

Okamoto‐Uchida, Y., Izawa, J., Nishimura, A., Hattori, A., Suzuki, N., & Hirayama, J. (2019) · Current Genomics · doi:10.2174/1389202919666191014094349 · Cited by 37

A molecular circadian clock operates in the parathyroid gland and is disturbed in chronic kidney disease associated bone and mineral disorder

Egstrand, S., Nordholm, A., Morevati, M., Mace, M. L., Hassan, A., Naveh‐Many, T., Rukov, J. L., Gravesen, E., Ølgaard, K., & Lewin, E. (2020) · Kidney International · doi:10.1016/j.kint.2020.06.034 · Cited by 36

Phosphorylation Hypothesis of Sleep

Ode, K. L., & Ueda, H. R. (2020) · Frontiers in Psychology · doi:10.3389/fpsyg.2020.575328 · Cited by 38

Circadian regulation of cellular physiology

Peek, C. B., Ramsey, K. M., Levine, D. C., Marcheva, B., Perelis, M., & Bass, J. (2015) · Methods in Enzymology · doi:10.1016/bs.mie.2014.10.006 · Cited by 35

Analysis of mammalian circadian clock protein complexes over a circadian cycle

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The role of circadian rhythm regulator PERs in oxidative stress, immunity, and cancer development

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The molecular clock as a metabolic rheostat

Perelis, M., Ramsey, K. M., & Bass, J. T. (2015) · Diabetes Obesity and Metabolism · doi:10.1111/dom.12521 · Cited by 36

Circadian regulation of renal function and potential role in hypertension

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Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

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Circadian rhythms in parasites

Rijo‐Ferreira, F., Takahashi, J. S., & Figueiredo, L. M. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006590 · Cited by 37

The NRON complex controls circadian clock function through regulated PER and CRY nuclear translocation

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The tail of cryptochromes: an intrinsically disordered cog within the mammalian circadian clock

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Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock

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