The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
Open accessAbstract
Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene Pseudo-Response Regulator 9 was repressed by an evening gene, previously identified with Timing Of CAB Expression1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A synthetic oscillatory network of transcriptional regulators
Elowitz, M. B., & Leibler, S. (2000) · Nature · doi:10.1038/35002125 · Cited by 4,630
Plant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage
Dodd, A. N., Salathia, N., Hall, A., Kévei, E., Tóth, R., Nagy, F., Hibberd, J. M., Millar, A. J., & Webb, A. A. R. (2005) · Science · doi:10.1126/science.1115581 · Cited by 1,487
Self-citationReciprocal Regulation Between TOC1 and LHY / CCA1 Within the Arabidopsis Circadian Clock
Alabadı́, D., Oyama, T., Yanovsky, M. J., Harmon, F. G., Más, P., & Kay, S. A. (2001) · Science · doi:10.1126/science.1061320 · Cited by 1,161
FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis
Sawa, M., Nusinow, D. A., Kay, S. A., & Imaizumi, T. (2007) · Science · doi:10.1126/science.1146994 · Cited by 909
The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth
Nusinow, D. A., Helfer, A., Hamilton, E. E., King, J. J., Imaizumi, T., Schultz, T. F., Farré, E. M., & Kay, S. A. (2011) · Nature · doi:10.1038/nature10182 · Cited by 907
Fowler, S. (1999) · The EMBO Journal · doi:10.1093/emboj/18.17.4679 · Cited by 814
Le Novere, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj092 · Cited by 762
The Circadian System in Higher Plants
Harmer, S. L. (2009) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.043008.092054 · Cited by 719
Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops
Tsai, T. Y.-C., Choi, Y. S., Ma, W., Pomerening, J. R., Tang, C., & Ferrell, J. E. (2008) · Science · doi:10.1126/science.1156951 · Cited by 690
LHY and CCA1 Are Partially Redundant Genes Required to Maintain Circadian Rhythms in Arabidopsis
Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H.-R., Carré, I. A., & Coupland, G. (2002) · Developmental Cell · doi:10.1016/s1534-5807(02)00170-3 · Cited by 638
Circadian Clock Mutants in Arabidopsis Identified by Luciferase Imaging
Millar, A. J., Carré, I. A., Strayer, C. A., Chua, N.-H., & Kay, S. A. (1995) · Science · doi:10.1126/science.7855595 · Cited by 604
Self-citationControl of Circadian Rhythms and Photoperiodic Flowering by the Arabidopsis GIGANTEA Gene
Park, D. H., Somers, D. E., Kim, Y. S., Choy, Y. H., Lim, H. K., Soh, M. S., Kim, H. J., Kay, S. A., & Nam, H. G. (1999) · Science · doi:10.1126/science.285.5433.1579 · Cited by 592
ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light
Kim, W.-Y., Fujiwara, S., Suh, S.-S., Kim, J., Kim, Y., Han, L., David, K., Putterill, J., Nam, H. G., & Somers, D. E. (2007) · Nature · doi:10.1038/nature06132 · Cited by 591
Nakamichi, N., Kiba, T., Henriques, R., Mizuno, T., Chua, N., & Sakakibara, H. (2010) · The Plant Cell · doi:10.1105/tpc.109.072892 · Cited by 587
Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana
Más, P., Kim, W.-Y., Somers, D. E., & Kay, S. A. (2003) · Nature · doi:10.1038/nature02163 · Cited by 580
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor
Gendron, J. M., Pruneda-Paz, J. L., Doherty, C. J., Gross, A. M., Kang, S. E., & Kay, S. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200355109 · Cited by 540
The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana
Doyle, M. R., Davis, S. J., Bastow, R. M., McWatters, H. G., Kozma-Bognár, L., Nagy, F., Millar, A. J., & Amasino, R. M. (2002) · Nature · doi:10.1038/nature00954 · Cited by 494
Self-citationClocks not winding down: unravelling circadian networks
Zhang, E. E., & Kay, S. A. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2995 · Cited by 446
Overlapping and Distinct Roles of PRR7 and PRR9 in the Arabidopsis Circadian Clock
Farré, E. M., Harmer, S. L., Harmon, F. G., Yanovsky, M. J., & Kay, S. A. (2005) · Current Biology · doi:10.1016/j.cub.2004.12.067 · Cited by 443
LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms
Hazen, S. P., Schultz, T. F., Pruneda-Paz, J. L., Borevitz, J. O., Ecker, J. R., & Kay, S. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503029102 · Cited by 441
Locke, J. C. W., Kozma‐Bognár, L., Gould, P. D., Fehér, B., Kevei, É., Nagy, F., Turner, M. S., Hall, A., & Millar, A. J. (2006) · Molecular Systems Biology · doi:10.1038/msb4100102 · Cited by 427
Self-citationCOP1 and ELF3 Control Circadian Function and Photoperiodic Flowering by Regulating GI Stability
Yu, J.-W., Rubio, V., Lee, N.-Y., Bai, S., Lee, S.-Y., Kim, S.-S., Liu, L., Zhang, Y., Irigoyen, M. L., Sullivan, J. A., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.09.026 · Cited by 425
Conditional Circadian Dysfunction of the Arabidopsis early-flowering 3 Mutant
Hicks, K. A., Millar, A. J., Carré, I. A., Somers, D. E., Straume, M., Meeks-Wagner, D. R., & Kay, S. A. (1996) · Science · doi:10.1126/science.274.5288.790 · Cited by 405
Self-citationExtension of a genetic network model by iterative experimentation and mathematical analysis
Locke, J. C. W., Southern, M. M., Kozma‐Bognár, L., Hibberd, V., Brown, P. E., Turner, M. S., & Millar, A. J. (2005) · Molecular Systems Biology · doi:10.1038/msb4100018 · Cited by 386
Self-citationThe Molecular Basis of Temperature Compensation in the Arabidopsis Circadian Clock
Gould, P. D., Locke, J. C. W., Larue, C., Southern, M. M., Davis, S. J., Hanano, S., Moyle, R., Milich, R., Putterill, J., Millar, A. J., et al. (2006) · The Plant Cell · doi:10.1105/tpc.105.039990 · Cited by 359
Self-citationThe ELF3 zeitnehmer regulates light signalling to the circadian clock
McWatters, H. G., Bastow, R. M., Hall, A., & Millar, A. J. (2000) · Nature · doi:10.1038/35047079 · Cited by 350
Self-citationLiu, X. L. (2001) · THE PLANT CELL ONLINE · doi:10.1105/tpc.13.6.1293 · Cited by 334
Salomé, P. A., & McClung, C. R. (2005) · The Plant Cell · doi:10.1105/tpc.104.029504 · Cited by 328
ELF3 Modulates Resetting of the Circadian Clock in Arabidopsis
Covington, M. F., Panda, S., Liu, X. L., Strayer, C. A., Wagner, D. R., & Kay, S. A. (2001) · The Plant Cell · doi:10.1105/tpc.000561 · Cited by 323
Helfer, A., Nusinow, D. A., Chow, B. Y., Gehrke, A. R., Bulyk, M. L., & Kay, S. A. (2011) · Current Biology · doi:10.1016/j.cub.2010.12.021 · Cited by 308
The Regulation of Circadian Period by Phototransduction Pathways in Arabidopsis
Millar, A. J., Straume, M., Chory, J., Chua, N.-H., & Kay, S. A. (1995) · Science · doi:10.1126/science.7855596 · Cited by 280
Self-citationDual Role of TOC1 in the Control of Circadian and Photomorphogenic Responses in Arabidopsis[W]
Más, P., Alabadí, D., Yanovsky, M. J., Oyama, T., & Kay, S. A. (2003) · The Plant Cell · doi:10.1105/tpc.006734 · Cited by 268
Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function
Ukai-Tadenuma, M., Yamada, R. G., Xu, H., Ripperger, J. A., Liu, A. C., & Ueda, H. R. (2011) · Cell · doi:10.1016/j.cell.2010.12.019 · Cited by 263
F-Box Proteins FKF1 and LKP2 Act in Concert with ZEITLUPE to Control Arabidopsis Clock Progression
Baudry, A., Ito, S., Song, Y. H., Strait, A. A., Kiba, T., Lu, S., Henriques, R., Pruneda-Paz, J. L., Chua, N.-H., Tobin, E. M., et al. (2010) · The Plant Cell · doi:10.1105/tpc.109.072843 · Cited by 250
Somers, D. E., Kim, W.-Y., & Geng, R. (2004) · The Plant Cell · doi:10.1105/tpc.016808 · Cited by 236
Fujiwara, S., Wang, L., Han, L., Suh, S.-S., Salomé, P. A., McClung, C. R., & Somers, D. E. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803471200 · Cited by 230
Matsushika, A., Makino, S., Kojima, M., Yamashino, T., & Mizuno, T. (2002) · Plant and Cell Physiology · doi:10.1093/pcp/pcf006 · Cited by 226
Temporal Repression of Core Circadian Genes Is Mediated through EARLY FLOWERING 3 in Arabidopsis
Dixon, L. E., Knox, K., Kozma‐Bognár, L., Southern, M. M., Pokhilko, A. V., & Millar, A. J. (2011) · Current Biology · doi:10.1016/j.cub.2010.12.013 · Cited by 223
Self-citationChen, H., Huang, X., Gusmaroli, G., Terzaghi, W., Lau, O. S., Yanagawa, Y., Zhang, Y., Li, J., Lee, J.-H., Zhu, D., et al. (2010) · The Plant Cell · doi:10.1105/tpc.109.065490 · Cited by 210
Harmer, S. L., & Kay, S. A. (2005) · The Plant Cell · doi:10.1105/tpc.105.033035 · Cited by 209
Pseudo-Response Regulators (PRRs) or True Oscillator Components (TOCs)
Mizuno, T., & Nakamichi, N. (2005) · Plant and Cell Physiology · doi:10.1093/pcp/pci087 · Cited by 204
PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock
Onai, K., & Ishiura, M. (2005) · Genes to Cells · doi:10.1111/j.1365-2443.2005.00892.x · Cited by 202
ELF3 Modulates Resetting of the Circadian Clock in Arabidopsis
Covington, M. F. (2001) · THE PLANT CELL ONLINE · doi:10.1105/tpc.13.6.1305 · Cited by 200
Makino, S., Matsushika, A., Kojima, M., Yamashino, T., & Mizuno, T. (2002) · Plant and Cell Physiology · doi:10.1093/pcp/pcf005 · Cited by 196
A comparative analysis of synthetic genetic oscillators
Purcell, O., Savery, N. J., Grierson, C. S., & di Bernardo, M. (2010) · Journal of The Royal Society Interface · doi:10.1098/rsif.2010.0183 · Cited by 192
Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY
Kim, J.-Y. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg075 · Cited by 169
Pokhilko, A., Hodge, S. K., Stratford, K., Knox, K., Edwards, K. D., Thomson, A. W., Mizuno, T., & Millar, A. J. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.69 · Cited by 159
Self-citationWang, L., Fujiwara, S., & Somers, D. E. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.76 · Cited by 143
Understanding systems-level properties: timely stories from the study of clocks
Hogenesch, J. B., & Ueda, H. R. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2972 · Cited by 141
How a cyanobacterium tells time
Dong, G., & Golden, S. S. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.10.003 · Cited by 115
Integrating ELF4 into the circadian system through combined structural and functional studies
Kolmos, E., Nowak, M., Werner, M., Fischer, K., Schwarz, G., Mathews, S., Schoof, H., Nagy, F., Bujnicki, J. M., & Davis, S. J. (2009) · HFSP journal · doi:10.2976/1.3218766 · Cited by 111
Liu, X. L., Covington, M. F., Fankhauser, C. D., Chory, J., & Wagner, D. R. (2001) · The Plant Cell · doi:10.2307/3871296 · Cited by 99
Ding, Z., Doyle, M. R., Amasino, R. M., & Davis, S. J. (2007) · Genetics · doi:10.1534/genetics.107.072769 · Cited by 97
Forward Genetic Analysis of the Circadian Clock Separates the Multiple Functions of ZEITLUPE
Kevei, É., Gyula, P., Hall, A. J. W., Kozma‐Bognár, L., Kim, W., Eriksson, M. E., Tóth, R., Hanano, S., Fehér, B., Southern, M. M., et al. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.074864 · Cited by 91
Self-citationHSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE
Kim, T.-S., Kim, W. Y., Fujiwara, S., Kim, J., Cha, J., Park, J., Lee, S. Y., & Somers, D. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110406108 · Cited by 84
Light inputs shape the Arabidopsis circadian system
Wenden, B., Kozma‐Bognár, L., Edwards, K. D., Hall, A. J. W., Locke, J. C. W., & Millar, A. J. (2011) · The Plant Journal · doi:10.1111/j.1365-313x.2011.04505.x · Cited by 76
Self-citationUbiquitin ligase switch in plant photomorphogenesis: A hypothesis
Pokhilko, A. V., Ramos, J. A., Holtan, H., Maszle, D. R., Khanna, R., & Millar, A. J. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.11.021 · Cited by 31
Self-citationO'Neill, J. S., Gerben Van Ooijen, A., Bihan, T. L., & Millar, A. J. (2011) · Journal of Biological Rhythms · doi:10.1177/0748730410397465 · Cited by 14
Self-citation
Cited by
Plant Flavoprotein Photoreceptors
Christie, J. M., Blackwood, L., Petersen, J., & Sullivan, S. (2015) · Plant and Cell Physiology · doi:10.1093/pcp/pcu196 · Cited by 294
Evolution of circadian rhythms: from bacteria to human
Bhadra, U., Thakkar, N., Das, P., & Pal Bhadra, M. (2017) · Sleep Medicine · doi:10.1016/j.sleep.2017.04.008 · Cited by 167
Abundant clock proteins point to missing molecular regulation in the plant circadian clock
(2025) · doi:10.1038/s44320-025-00086-5 · Cited by 4
Metadata
- Authors
- Pokhilko, A., Fernández, A. P., Edwards, K. D., Southern, M. M., Halliday, K. J., & Millar, A. J.
- Venue
- Molecular Systems Biology
- Published
- 2012-01
- Volume
- 8
- Issue
- 1
- Pages
- 574-574
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W2156444576
- Cited by
- 409
- References
- 58
- FWCI
- 57.02
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
