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Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis

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Abstract

A circadian rhythm is a roughly 24-h cycle in biological processes and physiological phenomena such as sleep, feeding, and photosynthesis for many organisms on Earth. The circadian patterns are coordinated by rhythmical gene expression of clock genes. Time-course transcriptomic analyses involving statistical methods have shown coordination of periodic gene expression in many organisms. Here we applied the cosine fitting method COSOPT to identify novel oscillating genes in microarray data for the chordate Ciona intestinalis. This organism showed rhythmic oxygen consumption in our previous study, but there were few homologous clock genes showing rhythmic mRNA expression. To understand circadian behavior at the transcriptomic level, we analyzed the 817 of 21,938 probes showing a 23- to 25-h period by means of COSOPT. Coupling the analysis of period detection with functional annotations indicated that previously unknown rhythmic mRNA expression might exist in C. intestinalis. In addition, we are releasing our implementation of COSOPT by means of R and C. All source code and supplementary information are available from https://github.com/mhiromi/cosopt.

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References

  1. Gallego M, Virshup D (2007) Post-translational modifications regulate the ticking of the circadian clock. Nat Rev Mol Cell Biol 8:139–148

    Article  Google Scholar 

  2. Panda S, Antoch MP, Miller BH et al (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109:307–320

    Article  Google Scholar 

  3. Ceriani MF, Hogenesch JB, Yanovsky M et al (2002) Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J Neurosci 22:9305–9319

    Google Scholar 

  4. Akhtar RA, Reddy AB, Maywood ES et al (2002) Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol 12:540–550

    Article  Google Scholar 

  5. Dehal P, Satou Y, Campbell RK et al (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298(80):2157–2167

    Article  Google Scholar 

  6. Rubin E, Shemesh Y, Cohen M et al (2006) Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock. Genome Res 16:1352–1365

    Article  Google Scholar 

  7. Imai KS, Hino K, Yagi K et al (2004) Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development 131:4047–4058. doi:10.1242/dev.01270

    Article  Google Scholar 

  8. Minamoto T, Hanai S, Kadota K et al (2010) Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption. J Biochem 147:175–184

    Article  Google Scholar 

  9. Straume M (2004) DNA microarray time series analysis : automated statistical assessment of circadian rhythms in gene expression patterning introduction. Methods Enzymol 383:149–166

  10. Satou Y, Mineta K, Ogasawara M et al (2008) Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 9:R152

    Article  Google Scholar 

  11. Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80. doi:10.1186/gb-2004-5-10-r80

    Article  Google Scholar 

  12. Oster H (2006) Transcriptional profiling in the adrenal gland reveals circadian regulation of hormone biosynthesis genes and nucleosome assembly genes. J Biol Rhythms 21:350–361

    Article  Google Scholar 

  13. Tassy O, Dauga D, Daian F et al (2010) The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Genome Res 20:1459–1468. doi:10.1101/gr.108175.110

    Article  Google Scholar 

  14. Erives A, Corbo JC, Levine M (1998) Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Dev Biol 225:213–225

    Article  Google Scholar 

  15. Panda S, Hogenesch JB, Kay SA (2002) Circadian rhythms from flies to human. Nature 417:329–335. doi:10.1038/417329a

    Article  Google Scholar 

  16. Pieper AA, Wu X, Han TW et al (2005) The neuronal PAS domain protein 3 transcription factor controls FGF-mediated adult hippocampal neurogenesis in mice. Proc Natl Acad Sci 102:14052–14057

  17. Pickard BS, Christoforou A, Thomson PA et al (2008) Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder. Mol Psychiatry. doi:10.1038/mp.2008.24

    MATH  Google Scholar 

  18. Sasakura Y, Mita K, Ogura Y, Horie T (2012) Ascidians as excellent chordate models for studying the development of the nervous system during embryogenesis and metamorphosis. Dev Growth Differ 54:420–437. doi:10.1111/j.1440-169X.2012.01343.x

    Article  Google Scholar 

  19. Takimoto N, Kusakabe T, Tsuda M (2007) Origin of the vertebrate visual cycle. Photochem Photobiol 83:242–247. doi:10.1562/2006-06-30-IR-957

    Article  Google Scholar 

  20. Boppana S, Scheglov A, Geffers R, Tarabykin V (2012) Cellular retinaldehyde-binding protein (CRALBP) is a direct downstream target of transcription factor Pax6. Biochim Biophys Acta Gen Subj. doi:10.1016/j.bbagen.2011.09.015

    MATH  Google Scholar 

  21. Glossop N, Gummadova J, Ghangrekar I, Hardin P, Coutts G (2014) Effects of TWIN-OF-EYELESS on clock gene expression and central-pacemaker neuron development in drosophila. J Biol Rhythms 29:151–166

    Article  Google Scholar 

  22. Knowles A, Koh K, Wu J-T et al (2009) The COP9 signalosome is required for light-dependent timeless degradation and Drosophila clock resetting. J Neurosci 29:1152–1162. doi:10.1523/JNEUROSCI.0429-08.2009

    Article  Google Scholar 

  23. Rajan KE, Rajkumar R, Liao C-C et al (2010) Light-induced COP9 signalosome expression in the Indian false vampire bat Megaderma lyra. J Physiol Sci 60:43–49. doi:10.1007/s12576-009-0064-4

    Article  Google Scholar 

  24. Tsutsui H, Oka Y (2000) Light-sensitive voltage responses in the neurons of the cerebral ganglion of Ciona savignyi (Chordata: Ascidiacea). Biol Bull 198:26–28

  25. Tsutsui H, Yamamoto N, Ito H, Oka Y (1998) GnRH-immunoreactive neuronal system in the presumptive ancestral chordate, Ciona intestinalis (Ascidian). Gen Comp Endocrinol 112:426–432

    Article  Google Scholar 

  26. Kawada T, Aoyama M, Okada I et al (2009) A novel inhibitory gonadotropin-releasing hormone-related neuropeptide in the ascidian, Ciona intestinalis. Peptides 30:2200–2205

    Article  Google Scholar 

  27. Shoguchi E, Hamada M, Fujie M, Satoh N (2011) Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis. Genesis 49:662–672

    Article  Google Scholar 

  28. Matsumae H, Hamada M, Fujie M et al (2013) A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis. Gene 519:82–90. doi:10.1016/j.gene.2013.01.042

    Article  Google Scholar 

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Author information

Author notes

  1. Hiromi Matsumae

    Present address: Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland

  2. Ryosuke Ishiwata

    Present address: Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, 4648601, Japan

Authors and Affiliations

  1. Department of Bioinformatics, Tokyo Medical and Dental University, Tokyo, Japan

    Hiromi Matsumae, Ryosuke Ishiwata & Hiroshi Tanaka

  2. Graduate School of Human Development and Environment, Kobe University, Kobe, Japan

    Toshifumi Minamoto

  3. Ishida Gr. of Clock Gene, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan

    Norio Ishida

  4. Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan

    Norio Ishida

  5. Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan

    Soichi Ogishima & Hiroshi Tanaka

Authors
  1. Hiromi Matsumae
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  2. Ryosuke Ishiwata
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  3. Toshifumi Minamoto
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  4. Norio Ishida
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  5. Soichi Ogishima
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  6. Hiroshi Tanaka
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Corresponding author

Correspondence to Hiromi Matsumae.

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Matsumae, H., Ishiwata, R., Minamoto, T. et al. Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis . Artif Life Robotics 20, 347–352 (2015). https://doi.org/10.1007/s10015-015-0237-6

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  • DOI: https://doi.org/10.1007/s10015-015-0237-6

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