Circadian cycles of gene expression in the coral, Acropora millepora
Open accessAbstract
BACKGROUND: Circadian rhythms regulate many physiological, behavioral and reproductive processes. These rhythms are often controlled by light, and daily cycles of solar illumination entrain many clock regulated processes. In scleractinian corals a number of different processes and behaviors are associated with specific periods of solar illumination or non-illumination--for example, skeletal deposition, feeding and both brooding and broadcast spawning. METHODOLOGY/PRINCIPAL FINDINGS: We have undertaken an analysis of diurnal expression of the whole transcriptome and more focused studies on a number of candidate circadian genes in the coral Acropora millepora using deep RNA sequencing and quantitative PCR. Many examples of diurnal cycles of RNA abundance were identified, some of which are light responsive and damped quickly under constant darkness, for example, cryptochrome 1 and timeless, but others that continue to cycle in a robust manner when kept in constant darkness, for example, clock, cryptochrome 2, cycle and eyes absent, indicating that their transcription is regulated by an endogenous clock entrained to the light-dark cycle. Many other biological processes that varied between day and night were also identified by a clustering analysis of gene ontology annotations. CONCLUSIONS/SIGNIFICANCE: Corals exhibit diurnal patterns of gene expression that may participate in the regulation of circadian biological processes. Rhythmic cycles of gene expression occur under constant darkness in both populations of coral larvae that lack zooxanthellae and in individual adult tissue containing zooxanthellae, indicating that transcription is under the control of a biological clock. In addition to genes potentially involved in regulating circadian processes, many other pathways were found to display diel cycles of transcription.
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
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Further studies employing artificial illumination mimicking both light/dark cycles and moonlight provided conflicting results for some of the above-mentioned data collected under natural light conditions.
“It has to be noted that further studies employing artificial illumination mimicking both light/dark cycles and moonlight provided conflicting results for some of the above-mentioned data collected under natural light conditions.”
From The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks (2020) · cites this paper as [31]
In Acropora millepora, only cry1 (but not cry2) was affected by exposure to DD, whereas cry2 increased under natural moonlight compared to artificial one during both LQM and FM.
“For instance, only cry1 (but not cry2) was affected by exposure to DD, whereas, although not significantly, cry2 increased under natural moonlight compared to the artificial one during both LQM and FM [27,31].”
From The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks (2020) · cites this paper as [31]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Humana Press eBooks · doi:10.1385/1-59259-192-2:365 · Cited by 14,952 · see citing works
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works
A Greedy Algorithm for Aligning DNA Sequences
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459 · see citing works
Mutation of the mouse klotho gene leads to a syndrome resembling ageing
Kuro-o, M., Matsumura, Y., Aizawa, H., Kawaguchi, H., Suga, T., Utsugi, T., Ohyama, Y., Kurabayashi, M., Kaname, T., Kume, E., et al. (1997) · Nature · doi:10.1038/36285 · Cited by 3,837 · see citing works
Dibner, C., Schibler, U., & Albrecht, U. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135821 · Cited by 2,421 · see citing works
Chronobiology: biological timekeeping
(2004) · Choice Reviews Online · doi:10.5860/choice.41-2795 · Cited by 679 · see citing works
Bioinformatics Methods and Protocols
Misener, S., & Krawetz, S. A. (1999) · Humana Press eBooks · doi:10.1385/1592591922 · Cited by 579 · see citing works
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479 · see citing works
Cycling vrille Expression Is Required for a Functional Drosophila Clock
Blau, J., & Young, M. W. (1999) · Cell · doi:10.1016/s0092-8674(00)81554-8 · Cited by 439 · see citing works
Sehgal, A., Rothenfluh, A., Hunter-Ensor, M., Chen, Y.-F., Myers, M. P., & Young, M. W. (1995) · Science · doi:10.1126/science.270.5237.808 · Cited by 370 · see citing works
A molecular switch for photoperiod responsiveness in mammals
Dardente, H., Wyse, C. A., Birnie, M. J., Dupré, S. M., Loudon, A. S. I., Lincoln, G. A., & Hazlerigg, D. G. (2010) · Current Biology · doi:10.1016/j.cub.2010.10.048 · Cited by 291 · see citing works
The F-box protein Slimb controls the levels of clock proteins Period and Timeless
Grima, B., Lamouroux, A., Chélot, E., Papin, C., Limbourg‐Bouchon, B., & Rouyer, F. (2002) · Nature · doi:10.1038/nature01122 · Cited by 288 · see citing works
Levy, O., Appelbaum, L., Leggat, W., Gothlif, Y., Hayward, D. C., Miller, D. J., & Hoegh-Guldberg, O. (2007) · Science · doi:10.1126/science.1145432 · Cited by 263 · see citing works
A PERSISTENT DIURNAL RHYTHM OF LUMINESCENCE IN GONYAULAX POLYEDRA
Hastings, J. W., & Sweeney, B. M. (1958) · Biological Bulletin · doi:10.2307/1539108 · Cited by 249 · see citing works
Food-anticipatory circadian rhythms: concepts and methods
Mistlberger, R. E. (2009) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2009.06965.x · Cited by 224 · see citing works
Patterns in the mass spawning of corals on the Great Barrier Reef from 1981 to 1984
Willis, B., Babcock, R. C., Harrison, P. L., et al. (1985) · ResearchOnline at James Cook University (James Cook University) · Cited by 221 · see citing works
Bae, K., Lee, C., Sidote, D. J., Chuang, K.-Y., & Edery, I. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.10.6142 · Cited by 221 · see citing works
Complex Diel Cycles of Gene Expression in Coral-Algal Symbiosis
Levy, O., Kaniewska, P., Alon, S., Eisenberg, E., Karako‐Lampert, S., Bay, L. K., Reef, R., Rodríguez‐Lanetty, M., Miller, D. J., & Hoegh‐Guldberg, O. (2011) · Science · doi:10.1126/science.1196419 · Cited by 137 · see citing works
Acute Induction of Eya3 by Late-Night Light Stimulation Triggers TSHβ Expression in Photoperiodism
Masumoto, K.-H., Ukai-Tadenuma, M., Kasukawa, T., Nagano, M., Uno, K. D., Tsujino, K., Horikawa, K., Shigeyoshi, Y., & Ueda, H. R. (2010) · Current Biology · doi:10.1016/j.cub.2010.11.038 · Cited by 118 · see citing works
Reitzel, A. M., Behrendt, L., & Tarrant, A. M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012805 · Cited by 96 · see citing works
Transcriptional regulation by a circadian rhythm.
Taylor, W. C. (1989) · The Plant Cell · doi:10.1105/tpc.1.2.259 · Cited by 74 · see citing works
Circadian clock gene expression in the coral Favia fragum over diel and lunar reproductive cycles
Hoadley, K. D., Szmant, A. M., & Pyott, S. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019755 · Cited by 71 · see citing works
Chronobiology: Biological Timekeeping
Giebultowicz, J. M. (2004) · Integrative and Comparative Biology · doi:10.1093/icb/44.3.266 · Cited by 68 · see citing works
Neural basis of timing and anticipatory behaviors
Antle, M. C., & Silver, R. (2009) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2009.06959.x · Cited by 65 · see citing works
Diel patterns of larval release by five brooding scleractinian corals
Fan, T., Lin, K., Kuo, F., Soong, K., Liu, L., & Fang, L. (2006) · Marine Ecology Progress Series · doi:10.3354/meps321133 · Cited by 62 · see citing works
Time-of-Day-Dependent Enhancement of Adult Neurogenesis in the Hippocampus
Tamai, S.-I., Sanada, K., & Fukada, Y. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003835 · Cited by 62 · see citing works
Urban, A. E., Zhou, X., Ungos, J. M., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.04.469 · Cited by 55 · see citing works
Transcriptome Analysis of the Circadian Regulatory Network in the Coral Acropora millepora
Vize, P. D. (2009) · Biological Bulletin · doi:10.1086/bblv216n2p131 · Cited by 48 · see citing works
Self-citationIn vitro establishment of symbiosis in Acropora millepora planulae
van Oppen, M. J. H. (2001) · Coral Reefs · doi:10.1007/s003380100167 · Cited by 44 · see citing works
CIRCADIAN RHYTHMS IN CORALS, PARTICULARLY FUNGIIDAE
Sweeney, B. M. (1976) · Biological Bulletin · doi:10.2307/1540717 · Cited by 40 · see citing works
Transcriptome analysis of the zebrafish pineal gland
Toyama, R., Chen, X., Jhawar, N., Aamar, E., Epstein, J., Reany, N., Alon, S., Gothilf, Y., Klein, D. C., & Dawid, I. B. (2009) · Developmental Dynamics · doi:10.1002/dvdy.21988 · Cited by 37 · see citing works
Tales from the Crypt(ochromes)
Gelder, R. N. V. (2002) · Journal of Biological Rhythms · doi:10.1177/074873002129002401 · Cited by 36 · see citing works
Anctil, M., Hayward, D. C., Miller, D. J., & Ball, E. E. (2006) · Gene · doi:10.1016/j.gene.2006.10.025 · Cited by 29 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks
Andreatta, G., & Tessmar-Raible, K. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.03.009 · Cited by 111 · see citing works
Lunar biological effects and the magnetosphere
Bevington, M. (2015) · Pathophysiology · doi:10.1016/j.pathophys.2015.08.005 · Cited by 50 · see citing works
Brady, A. K., Willis, B. L., Harder, L. D., & Vize, P. D. (2016) · The Biological Bulletin · doi:10.1086/bblv230n2p130 · Cited by 48 · see citing works
Self-citationTranscriptome dynamics over a lunar month in a broadcast spawning acroporid coral
Oldach, M. J., Workentine, M., Matz, M. V., Fan, T., & Vize, P. D. (2017) · Molecular Ecology · doi:10.1111/mec.14043 · Cited by 39 · see citing works
Self-citation
- Authors
- Brady, A. K., Snyder, K. A., & Vize, P. D.
- Affiliations
- University of Calgary (CA)
- Corresponding author
- Vize, Peter D.
- ORCID
- Vize, Peter D.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-09-19
- Volume
- 6
- Issue
- 9
- Pages
- e25072
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3176305
- OpenAlex
- W1996282927
- Cited by
- 56
- References
- 35
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 5 · 2023: 4 · 2022: 3 · 2021: 1 · 2020: 6 · 2019: 6 · 2018: 4 · 2017: 3 · 2016: 5 · 2015: 4 · 2014: 4 · 2013: 5 · 2012: 3
- FWCI
- 1.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- Alberta Innovates
- National Institutes of Health
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01 HD45776, R01HD045776, P41HD064556)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Physical Sciences › Environmental Science › Ecology › Coral and Marine Ecosystems Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
- Keywords
- circadian rhythm, diel gene expression, Acropora millepora, scleractinian corals, clock genes, cryptochrome, TIMELESS, cycle gene, eyes absent, light entrainment, constant darkness, coral larvae, zooxanthellae
- MeSH terms
- Animals, Biological Clocks, Circadian Rhythm, Darkness, Gene Expression Regulation, Light, RNA, Messenger, Biomarkers, Reverse Transcriptase Polymerase Chain Reaction, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Anthozoa, Real-Time Polymerase Chain Reaction
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
