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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TopHat: discovering splice junctions with RNA-Seq

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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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Preservation of circadian rhythms by the protein folding chaperone, BiP

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Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clockPreprint

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Biochemical mechanisms of period control within the mammalian circadian clock

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ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals

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Circadian mRNA expression: insights from modeling and transcriptomics

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Chromatin-based reprogramming of a courtship regulator by concurrent pheromone perception and hormone signaling

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Improved locomotor recovery after contusive spinal cord injury in Bmal1−/− mice is associated with protection of the blood spinal cord barrier

Słomnicki, Ł. P., Myers, S. A., Ohri, S. S., Parsh, M. V., Andres, K. R., Chariker, J. H., Rouchka, E. C., Whittemore, S. R., & Hetman, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-71131-6 · Cited by 31

Interactions among microbes, the immune system, and the circadian clock

Brooks, J. F., & Hooper, L. V. (2020) · Seminars in Immunopathology · doi:10.1007/s00281-020-00820-1 · Cited by 31

Dorsal striatum dopamine oscillations: Setting the pace of food anticipatory activity

de Lartigue, G., & McDougle, M. J. (2018) · Acta Physiologica · doi:10.1111/apha.13152 · Cited by 33

Deletion of Bmal1 Prevents Diet-Induced Ectopic Fat Accumulation by Controlling Oxidative Capacity in the Skeletal Muscle

Wada, T., Ichihashi, Y., Suzuki, E., Kosuge, Y., Ishige, K., Uchiyama, T., Makishima, M., Nakao, R., Oishi, K., & Shimba, S. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092813 · Cited by 34

A role for alternative splicing in circadian control of exocytosis and glucose homeostasisPreprint

Marcheva, B., Perelis, M., Weidemann, B. J., Taguchi, A., Lin, H., Omura, C., Kobayashi, Y., Newman, M. V., Wyatt, E. J., McNally, E. M., et al. (2020) · Genes & Development · doi:10.1101/gad.338178.120 · Cited by 33

The Liver in the Eyes of a Chronobiologist

Zwighaft, Z., Reinke, H., & Asher, G. (2016) · Journal of Biological Rhythms · doi:10.1177/0748730416633552 · Cited by 29

Opposing actions of Per1 and Cry2 in the regulation of Per1 target gene expression in the liver and kidney

Richards, J., All, S. C., Skopis, G., Cheng, K., Compton, B., Srialluri, N., Stow, L. R., Jeffers, L. A., & Gumz, M. L. (2013) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.00195.2013 · Cited by 31

Dawn of Epitranscriptomic Medicine

Gatsiou, A., & Stellos, K. (2018) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.118.001927 · Cited by 31

Chronobiology of limbic seizures: Potential mechanisms and prospects of chronotherapy for mesial temporal lobe epilepsy

Gitaí, D. L. G., de Andrade, T. G., dos Santos, Y. D. R., Attaluri, S., & Shetty, A. K. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.01.004 · Cited by 31

The circadian clock protects against ionizing radiation‐induced cardiotoxicity

Dakup, P., Porter, K. I., Gajula, R. P., Goel, P. N., Cheng, Z., & Gaddameedhi, S. (2020) · The FASEB Journal · doi:10.1096/fj.201901850rr · Cited by 32

Adolescent sleep timing and dietary patterns in relation to DNA methylation of core circadian genes: a pilot study of Mexican youth

Jansen, E. C., Dolinoy, D. C., Peterson, K. E., O'Brien, L. M., Chervin, R. D., Cantoral, A., Téllez‐Rojo, M. M., Solano-González, M., & Goodrich, J. M. (2020) · Epigenetics · doi:10.1080/15592294.2020.1827719 · Cited by 30

Entrainment Is NOT Synchronization: An Important Distinction and Its Implications

Bittman, E. L. (2020) · Journal of Biological Rhythms · doi:10.1177/0748730420972817 · Cited by 31

Circadian Misalignment and Metabolic Disorders: A Story of Twisted Clocks

Woller, A., & Gonze, D. (2021) · Biology · doi:10.3390/biology10030207 · Cited by 36

Circadian clock protein BMAL1 regulates melanogenesis through MITF in melanoma cells

Sarkar, S., Porter, K. I., Dakup, P., Gajula, R. P., Koritala, B. S. C., Hylton, R. K., Kemp, M. G., Wakamatsu, K., & Gaddameedhi, S. (2021) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12998 · Cited by 31

Epigenetic Clock and Circadian Rhythms in Stem Cell Aging and Rejuvenation

Samoilova, E. M., Викторович, Б. В., Ekusheva, E. V., Zhang, C., Troitskiy, A. V., & Baklaushev, V. P. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11111050 · Cited by 32

Dysregulation of Npas2 leads to altered metabolic pathways in a murine knockout model

O’Neil, D. S., Figueroa, H. M., Mistretta, T., Su, C., Lane, R. H., & Aagaard, K. M. (2013) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2013.08.015 · Cited by 32

Nuclear envelope protein MAN1 regulates clock through BMAL1

Lin, S., Zhang, L., Lin, X., Zhang, L. C., Garcia, V. E., Tsai, C.-W., Ptáček, L. J., & Fu, Y. (2014) · eLife · doi:10.7554/elife.02981 · Cited by 32

Circadian rhythm‐associated Rev‐erbα modulates polarization of decidual macrophage via the PI3K/Akt signaling pathway

Cui, L., Jin, X., Xu, F., Wang, S., Liu, L., Li, X., Lin, H., & Du, M. (2021) · American Journal of Reproductive Immunology · doi:10.1111/aji.13436 · Cited by 30

The analytical landscape of static and temporal dynamics in transcriptome data

Oh, S., Song, S., Dasgupta, N., & Grabowski, G. A. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00035 · Cited by 29

Quantitative live imaging of Venus::BMAL1 in a mouse model reveals complex dynamics of the master circadian clock regulator

Yang, N., Smyllie, N. J., Morris, H., Gonçalves, C. F., Dudek, M., Pathiranage, D. R., Chesham, J. E., Adamson, A. D., Spiller, D. G., Zindy, E., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008729 · Cited by 31

Expanding the link between circadian rhythms and redox metabolism of epigenetic control

Sato, T., & Greco, C. M. (2021) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2021.01.009 · Cited by 30

CRYPTOCHROMES promote daily protein homeostasis

Wong, D. C. S., Seinkmane, E., Zeng, A., Stangherlin, A., Rzechorzek, N. M., Beale, A. D., Day, J., Reed, M., Peak‐Chew, S. Y., Styles, C. T., et al. (2022) · The EMBO Journal · doi:10.15252/embj.2021108883 · Cited by 30

Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions

Asher, G., & Zhu, B. (2022) · Hepatology · doi:10.1002/hep.32580 · Cited by 28

CirGRDB: a database for the genome-wide deciphering circadian genes and regulators

Li, X., Shi, L., Zhang, K., Wei, W., Liu, Q., Mao, F., Li, J., Cai, W., Chen, H., Teng, H., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx944 · Cited by 35

Novel transcriptional networks regulated by CLOCK in human neuronsPreprint

Fontenot, M. R., Berto, S., Liu, Y., Werthmann, G. C., Douglas, C., Usui, N., Gleason, K., Tamminga, C. A., Takahashi, J. S., & Konopka, G. (2017) · Genes & Development · doi:10.1101/gad.305813.117 · Cited by 30

Circadian regulation of digestive and metabolic tissues

Taleb, Z., & Karpowicz, P. A. (2022) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00166.2022 · Cited by 30

Circadian regulation of liver metabolism: experimental approaches in human, rodent, and cellular models

Daniels, L. J., Kay, D., Marjot, T., Hodson, L., & Ray, D. W. (2023) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00551.2022 · Cited by 32

Circadian rhythms and metabolism: from the brain to the gut and back again

Cribbet, M. R., Logan, R. W., Edwards, M. D., Hanlon, E. C., Peek, C. B., Stubblefield, J. J., Vasudevan, S. R., Ritchey, F. C., & Frank, E. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13188 · Cited by 29

Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation

Miller, S., Srivastava, A., Nagai, Y., Aikawa, Y., Tama, F., & Hirota, T. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2026191118 · Cited by 30

MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer

Burchett, J. B., Knudsen-Clark, A. M., & Altman, B. J. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147761 · Cited by 32

Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice

Deng, L., Gao, B., Zhao, L., Zhang, Y., Zhang, Q., Guo, M., Yang, Y., Wang, S., Xie, L., Lou, H., et al. (2022) · Genome biology · doi:10.1186/s13059-021-02594-7 · Cited by 30

Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids

Umemura, Y. M., Koike, N., Tsuchiya, Y., Watanabe, H., Kondoh, G., Kageyama, R., & Yagita, K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114083119 · Cited by 31

Exome-wide screening identifies novel rare risk variants for major depression disorder

Cheng, S., Cheng, B., Liu, L., Yang, X., Meng, P., Yao, Y., Pan, C., Zhang, J., Li, C., Zhang, H., et al. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01536-4 · Cited by 28

Deciphering clock genes as emerging targets against aging

Zhu, Y., Liu, Y., Escames, G., Yang, Z. Z., Zhao, H., Lu, Q., Xue, C., Xu, D., Acuña-Castroviejo, D., & Yang, Y. (2022) · Ageing Research Reviews · doi:10.1016/j.arr.2022.101725 · Cited by 32

Inflammation o'clock: interactions of circadian rhythms with inflammation‐induced skeletal muscle atrophy

da Silva, F. M., Esser, K. A., Murach, K. A., & Greene, N. P. (2023) · The Journal of Physiology · doi:10.1113/jp284808 · Cited by 31

Circadian rhythms revealed: unraveling the genetic, physiological, and behavioral tapestry of the human biological clock and rhythms

Morin, R., Forest, G., & Imbeault, P. (2025) · Frontiers in Sleep · doi:10.3389/frsle.2025.1544945 · Cited by 35

Chromatin and signaling

Suganuma, T., & Workman, J. L. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.02.016 · Cited by 28

Ubiquitin ligase TRAF 2 attenuates the transcriptional activity of the core clock protein BMAL 1 and affects the maximal Per1 mRNA level of the circadian clock in cells

Chen, S., Yang, J., Yang, L., Zhang, Y., Zhou, L., Liu, Q. L., Duan, C., Mieres, C. A., Zhou, G., & Xu, G. (2018) · FEBS Journal · doi:10.1111/febs.14595 · Cited by 28

Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin

Park, J., & Belden, W. J. (2018) · BMC Genomics · doi:10.1186/s12864-018-5170-3 · Cited by 28

BMAL1 induces colorectal cancer metastasis by stimulating exosome secretion

Dong, P., Wang, Y.-P., Liu, Y., Zhu, C., Lin, J., Qian, R., Hua, L., & Lü, C. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06883-z · Cited by 30

Early doors ( Edo ) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking

Militi, S., Maywood, E. S., Sandate, C. R., Chesham, J. E., Barnard, A. R., Parsons, M. J., Vibert, J., Joynson, G., Partch, C. L., Hastings, M. H., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517549113 · Cited by 28

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes

Suzuki, T., Kikuguchi, C., Nishijima, S., Nagashima, T., Takahashi, A., Okada, M., & Yamamoto, T. (2019) · Development · doi:10.1242/dev.168146 · Cited by 28

Circadian clock-gastrointestinal peptide interaction in peripheral tissues and the brain

Landgraf, D., Neumann, A.-M., & Oster, H. (2017) · Best Practice & Research Clinical Endocrinology & Metabolism · doi:10.1016/j.beem.2017.10.007 · Cited by 26

Enriching the Circadian Proteome

Takahashi, J. S. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2016.12.014 · Cited by 27

JmjC domain proteins modulate circadian behaviors and sleep in Drosophila

Shalaby, N. A., Pinzón, J. H., Narayanan, A. S., Jin, E. J., Ritz, M. P., Dove, R., Wolfenberg, H., Rodan, A. R., Buszczak, M., & Rothenfluh, A. (2018) · Scientific Reports · doi:10.1038/s41598-017-18989-1 · Cited by 26

Sirt6 deacetylase activity regulates circadian rhythms via Per2

Sun, S., Liu, Z., Feng, Y., Shi, L., Cao, X., Cai, Y., & Liu, B. (2019) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2019.01.143 · Cited by 27

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

Brunet, A., Forsberg, F., Fan, Q., Sæther, T., & Collas, P. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00917 · Cited by 27

Decoding the function and regulation of the mammalian 12-h clock

Zhu, B. (2020) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjaa021 · Cited by 24

Statistical mechanics of clock gene networks underlying circadian rhythms

Sun, L., Dong, A., Griffin, C. H., & Wu, R. (2021) · Applied Physics Reviews · doi:10.1063/5.0029993 · Cited by 26

Circadian rhythms in the tissue-specificity from metabolism to immunity: insights from omics studies

Kinouchi, K., Mikami, Y., Kanai∥, T., & Itoh, H. (2021) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2021.100984 · Cited by 28

Circadian clock regulates developmental time through ecdysone and juvenile hormones in Bombyx mori

Qiu, J., Dai, T., Luo, C. Y., Cui, W., Liu, K., Li, J., Sima, Y., & Xu, S. (2023) · Insect Molecular Biology · doi:10.1111/imb.12835 · Cited by 27

A Novel Bmal1 Mutant Mouse Reveals Essential Roles of the C-Terminal Domain on Circadian Rhythms

Park, N., Kim, H.-D., Cheon, S., Row, H., Lee, J. Y., Han, D.-H., Cho, S., & Kim, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138661 · Cited by 24

Nucleotide excision repair efficiency in quiescent human fibroblasts is modulated by circadian clock

Bee, L., Marini, S., Pontarin, G., Ferraro, P., Costa, R., Albrecht, U., & Celotti, L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv081 · Cited by 27

HCFC2 is needed for IRF1- and IRF2-dependent Tlr3 transcription and for survival during viral infections

Sun, L., Jiang, Z., Acosta-Rodríguez, V. A., Berger, M., Du, X., Choi, J. H., Wang, J., Wang, K.-W., Kilaru, G., Mohawk, J. A., et al. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20161630 · Cited by 27

Histone deacetylase inhibitors induce the expression of tumor suppressor genes Per1 and Per2 in human gastric cancer cells

Hernández-Rosas, F., Hernández‐Oliveras, A., Flores‐Peredo, L., Rodr�guez, G., Zarain‐Herzberg, �., Caba, M., & Santiago-Garcı́a, J. (2018) · Oncology Letters · doi:10.3892/ol.2018.8851 · Cited by 27

Quantitative Studies for Cell-Division Cycle Control

Arata, Y., & Takagi, H. (2019) · Frontiers in Physiology · doi:10.3389/fphys.2019.01022 · Cited by 28

Epigenetic Signaling in Glia Controls Presynaptic Homeostatic Plasticity

Wang, T., Morency, D. T., Harris, N., & Davis, G. W. (2019) · Neuron · doi:10.1016/j.neuron.2019.10.041 · Cited by 25

Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice

Zhang, Y., Chen, G., Deng, L., Gao, B., Yang, J., Ding, C., Zhang, Q., Ouyang, W., Guo, M., Wang, W., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad658 · Cited by 26

Circadian coordination: understanding interplay between circadian clock and mitochondria

Kim, J., & Sun, W. (2024) · Animal Cells and Systems · doi:10.1080/19768354.2024.2347503 · Cited by 26

Regulation of metabolism by circadian rhythms: Support from time-restricted eating, intestinal microbiota & omics analysis

Xie, X., Zhang, M., & Luo, H. (2024) · Life Sciences · doi:10.1016/j.lfs.2024.122814 · Cited by 29

A glial circadian gene expression atlas reveals cell-type and disease-specific reprogramming in response to amyloid pathology or aging

Sheehan, P. W., Fass, S. B., Sapkota, D., Kang, S., Hollis, H. C., Lawrence, J. H., Park, S., Sharma, A., Schafer, D. P., Anafi, R. C., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-02067-1 · Cited by 30

Common features of circadian timekeeping in diverse organisms

Kumar, V., & Sharma, A. (2018) · Current Opinion in Physiology · doi:10.1016/j.cophys.2018.07.004 · Cited by 26

Amplitude Effects Allow Short Jet Lags and Large Seasonal Phase Shifts in Minimal Clock Models

Ananthasubramaniam, B., Schmal, C., & Herzel, H. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.01.014 · Cited by 26

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

Mermet, J., Yeung, J., & Naef, F. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009350 · Cited by 26

The hepatic circadian clock regulates the choline kinase α gene through the BMAL1-REV-ERBα axis

Gréchez‐Cassiau, A., Feillet, C. A., Guérin, S., & Delaunay, F. (2015) · Chronobiology International · doi:10.3109/07420528.2015.1046601 · Cited by 26

Predicted MicroRNAs for Mammalian Circadian Rhythms

Figueredo, D. D. S., Barbosa, M. R., Gitaí, D. L. G., & de Andrade, T. G. (2013) · Journal of Biological Rhythms · doi:10.1177/0748730413476827 · Cited by 26

Achilles is a circadian clock-controlled gene that regulates immune function in Drosophila

Li, J., Terry, E. E., Fejer, E., Gamba, D., Hartmann, N., Logsdon, J., Michalski, D., Rois, L. E., Scuderi, M. J., Kunst, M., et al. (2016) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2016.11.012 · Cited by 26

Systems Biology-Derived Discoveries of Intrinsic Clocks

Millius, A., & Ueda, H. R. (2017) · Frontiers in Neurology · doi:10.3389/fneur.2017.00025 · Cited by 27

Environmental and hormonal regulation of epigenetic enzymes in the hypothalamus

Stevenson, T. J. (2017) · Journal of Neuroendocrinology · doi:10.1111/jne.12471 · Cited by 26

Circadian de(regulation) in physiology: implications for disease and treatmentPreprint

de Assis, L. V. M., & Kramer, A. (2024) · Genes & Development · doi:10.1101/gad.352180.124 · Cited by 31

The metabolic significance of peripheral tissue clocks

Hunter, L., & Bechtold, D. A. (2025) · Communications Biology · doi:10.1038/s42003-025-07932-0 · Cited by 33

Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

Hoffmann, J. M., Symul, L., Shostak, A., Fischer, T., Naef, F., & Brunner, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102238 · Cited by 30

Circadian regulation of neutrophils: Control by a cell‐autonomous clock or systemic factors?

Ella, K., Mócsai, A., & Káldi, K. (2018) · European Journal of Clinical Investigation · doi:10.1111/eci.12965 · Cited by 26

Associations of clock genes polymorphisms with soft tissue sarcoma susceptibility and prognosis

Benna, C., Rajendran, S., Spiro, G., Tropea, S., Fiore, P. D., Rossi, C. R., & D, S. M. M. (2018) · Journal of Translational Medicine · doi:10.1186/s12967-018-1715-0 · Cited by 26

Understanding Quantitative Circadian Regulations Are Crucial Towards Advancing Chronotherapy

Chowdhury, D., Wang, C., Lü, A., & Zhu, H. (2019) · Cells · doi:10.3390/cells8080883 · Cited by 24

Diurnal Rhythmicity Programs of Microbiota and Transcriptional Oscillation of Circadian Regulator, NFIL3

Kubo, M. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.552188 · Cited by 26

Cold‐induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

Fischl, H., McManus, D., Oldenkamp, R., Schermelleh, L., Mellor, J., Jagannath, A., & Furger, A. (2020) · The EMBO Journal · doi:10.15252/embj.2020105604 · Cited by 26

Neonatal overfeeding during lactation rapidly and permanently misaligns the hepatic circadian rhythm and programmes adult NAFLD

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Circadian clocks, feeding time, and metabolic homeostasis

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