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Molecular Genetic and Genomic Analyses of Zebrafish Circadian Rhythmicity

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Biological Timekeeping: Clocks, Rhythms and Behaviour

Abstract

Evolving from long-term adaptation of life to the cyclic physical environment of the Earth, the circadian clock as endogenous and self-sustained time-keeping mechanisms plays modulatory roles in various fundamental life processes from molecular, biochemical, cellular, physiological, to behavioral levels. Circadian dysrhythmias lead to malfunctions of the body and numerous diseases. The zebrafish (Danio rerio) as an important animal model has recently become attractive for investigating regulatory mechanisms of vertebrate circadian clocks. In this chapter, we attempted to summarize the latest progresses of utilizing mutational analysis, transgenic technique, and transcriptome tools to delineate molecular genetic and genomic mechanisms underlying zebrafish circadian rhythmicity.

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Acknowledgment

This work was supported by the grants from the National Basic Research Program of China (973 Program) (2012CB947600), the National Natural Science Foundation of China (NSFC) (31030062), the Jiangsu Distinguished Professorship Program (SR13400111), the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions (YX13400214), the High-Level Innovative Team of Jiangsu Province, and the “333” Project of Jiangsu Province (BRA2015328). We wish to thank Dr. Nicolas Cermakian at the Douglas Mental Health University Institute and McGill University; Dr. Yoav Gothilf, Tel-Aviv University; and members of the Wang laboratory for their helpful comments on early versions of the chapter. Due to limited space, we regret that the works of many colleagues were not included in this chapter.

Author information

Authors and Affiliations

  1. Center for Circadian Clocks, Soochow University, Suzhou, 215123, China

    Zhaomin Zhong, Mingyong Wang, Guodong Huang, Shuqing Zhang & Han Wang

Authors
  1. Zhaomin Zhong
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  2. Mingyong Wang
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  3. Guodong Huang
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  4. Shuqing Zhang
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  5. Han Wang
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Corresponding author

Correspondence to Han Wang .

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Editors and Affiliations

  1. Department of Zoology, University of Delhi, Delhi, India

    Vinod Kumar

Appendices

Key Questions of Interest

  • What are advantages and disadvantages of zebrafish as a circadian model?

  • What are roles of zebrafish Per1b in maintaining circadian rhythms?

  • What are roles of zebrafish Per2 in maintaining circadian rhythms?

  • What are roles of zebrafish Clock1a in maintaining circadian rhythms?

Suggested Readings

2.1 Zebrafish Physiological and Behavioral Rhythms

Cahill GM, Hurd MW, Batchelor MM (1998) Circadian rhythmicity in the locomotor activity of larval zebrafish. Neuroreport 9:3445–3449

Liu C, Hu J, Qu C, Wang L, Huang G, Niu P, Zhong Z, Hong F, Wang G, Postlethwait JH, Wang H (2015) Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes. Sci Rep 5:8113

Rihel J, Prober DA, Arvanites A, Lam K, Zimmerman S, Jang S, Haggarty SJ, Kokel D, Rubin LL, Peterson RT, Schier AF (2010) Zebrafish behavioral profiling links drugs to biological targets and rest/wake regulation. Science 327:348–351

Vatine G, Vallone D, Gothilf Y, Foulkes NS (2011) It’s time to swim! Zebrafish and the circadian clock. FEBS Lett 585:1485–1494

2.2 Mutational Analysis of Zebrafish Circadian Rhythmicity

DeBruyne J, Hurd MW, Gutierrez L, Kaneko M, Tan Y, Wells DE, Cahill GM (2004) Isolation and phenogenetics of a novel circadian rhythm mutant in zebrafish. J Neurogenet 18:403–428

Huang J, Zhong Z, Wang M, Chen X, Tan Y, Zhang S, He W, He X, Huang G, Lu H, Wu P, Che Y, Yan YL, Postlethwait JH, Chen W, Wang H (2015) Circadian modulation of dopamine levels and dopaminergic neuron development contributes to attention deficiency and hyperactive behavior. J Neurosci 35:2572–2587

Tan Y, DeBruyne J, Cahill GM, Wells DE (2008) Identification of a mutation in the clock1 gene affecting zebrafish circadian rhythms. J Neurogenet 22:149–166

Wang M, Zhong Z, Zhong Y, Zhang W, Wang H (2015) The zebrafish period2 protein positively regulates the circadian clock through mediation of retinoic acid receptor (RAR)-related orphan receptor alpha (Roralpha). J Biol Chem 290:4367–4382

2.3 Transgenic Analysis of Zebrafish Circadian Rhythmicity

Gothilf Y, Coon SL, Toyama R, Chitnis A, Namboodiri MA, Klein DC (1999) Zebrafish serotonin N-acetyltransferase-2: marker for development of pineal photoreceptors and circadian clock function. Endocrinology 140:4895–4903

Kaneko M, Cahill GM (2005) Light-dependent development of circadian gene expression in transgenic zebrafish. PLoS Biol 3:e34

Weger M, Weger BD, Diotel N, Rastegar S, Hirota T, Kay SA, Strahle U, Dickmeis T (2013) Real-time in vivo monitoring of circadian e-box enhancer activity: a robust and sensitive zebrafish reporter line for developmental, chemical and neural biology of the circadian clock. Dev Biol 380:259–273

2.4 Transcriptome Analysis of Zebrafish Circadian Rhythmicity

Li Y, Li G, Wang H, Du J, Yan J (2013) Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish. PLoS Comput Biol 9:e1002940

Tovin A, Alon S, Ben-Moshe Z, Mracek P, Vatine G, Foulkes NS, Jacob-Hirsch J, Rechavi G, Toyama R, Coon SL, Klein DC, Eisenberg E, Gothilf Y (2012) Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork. PLoS Genet 8:e1003116

Weger BD, Sahinbas M, Otto GW, Mracek P, Armant O, Dolle D, Lahiri K, Vallone D, Ettwiller L, Geisler R, Foulkes NS, Dickmeis T (2011) The light responsive transcriptome of the zebrafish: function and regulation. PloS One 6:e17080

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Zhong, Z., Wang, M., Huang, G., Zhang, S., Wang, H. (2017). Molecular Genetic and Genomic Analyses of Zebrafish Circadian Rhythmicity. In: Kumar, V. (eds) Biological Timekeeping: Clocks, Rhythms and Behaviour. Springer, New Delhi. https://doi.org/10.1007/978-81-322-3688-7_8

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