The Community for Technology Leaders
RSS Icon
Issue No.01 - January-February (2011 vol.8)
pp: 108-121
Wenxue Wang , University of California Santa Barbara, Santa Barbara
Bijoy K. Ghosh , Texas Tech University, Lubbock
Himadri B. Pakrasi , Washington University in Saint Louis, Saint Louis
Behavior of living organisms is strongly modulated by the day and night cycle giving rise to a cyclic pattern of activities. Such a pattern helps the organisms to coordinate their activities and maintain a balance between what could be performed during the "day” and what could be relegated to the "night.” This cyclic pattern, called the "Circadian Rhythm,” is a biological phenomenon observed in a large number of organisms. In this paper, our goal is to analyze transcriptome data from Cyanothece for the purpose of discovering genes whose expressions are rhythmic. We cluster these genes into groups that are close in terms of their phases and show that genes from a specific metabolic functional category are tightly clustered, indicating perhaps a "preferred time of the day/night” when the organism performs this function. The proposed analysis is applied to two sets of microarray experiments performed under varying incident light patterns. Subsequently, we propose a model with a network of three phase oscillators together with a central master clock and use it to approximate a set of "circadian-controlled genes” that can be approximated closely.
Gene expression, circadian rhythm, microarray time series, diurnal cycle, phase oscillation, cyanothece, KaiC protein, oscillator network.
Wenxue Wang, Bijoy K. Ghosh, Himadri B. Pakrasi, "Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 1, pp. 108-121, January-February 2011, doi:10.1109/TCBB.2009.37
[1] S. Aoki, T. Kondo, and M. Ishiura, "A Promoter-Trap Vector for Clock-Controlled Genes in the Cyanobacterium Synechocystis sp. PCC 6803," J. Microbiological Methods, vol. 49, no. 3, pp. 265-274, 2002.
[2] K. Arita, H. Hashimoto, K. Igari, M. Akaboshi, S. Kutsuna, M. Sato, and T. Shimizu, "Structural and Biochemical Characterization of a Cyanobacterium Circadian Clock-Modifier Protein," J. Biological Chemistry, vol. 282, no. 2, pp. 1128-1135, 2007.
[3] D. Bell-Pedersen, V.M. Cassone, D.J. Earnest, S.S. Golden, P.E. Hardin, T.L. Thomas, and M.J. Zoran, "Circadian Rhythms from Multiple Oscillators: Lessons from Diverse Organisms," Nature Rev. Genetics, vol. 6, no. 7, pp. 544-556, 2005.
[4] E. Bunning, The Physiological Clock. Springer-Verlag, 1973.
[5] E.L. Campbell, M.L. Summers, H. Christman, M.E. Martin, and J.C. Meeks, "Global Gene Expression Patterns of Nostoc punctiforme in Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia," J. Bacteriology, vol. 189, no. 14, pp. 5247-5256, 2007.
[6] D.J. Chadwick and J.A. Goode, Molecular Clocks and Light Signalling. John Wiley & Sons, Ltd., 2003.
[7] T.H. Chen, T.L. Chen, L.M. Hung, and T.C. Huang, "Circadian Rhythm in Amino Acid Uptake by Synechococcus RF-1," Plant Physiology, vol. 97, no. 1, pp. 55-59, 1991.
[8] S. Clodong, U. Dühring, L. Kronk, A. Wilde, I. Axmann, H. Herzel, and M. Kollmann, "Functioning and Robustness of a Bacterial Circadian Clock," Molecular Systems Biology, vol. 3, article no. 90, 2007.
[9] J.C. Dunlap, J.J. Loros, and P.J. DeCoursey, Chronobiology: Biological Timekeeping. Sinauer Assoc., Inc., 2004.
[10] T.R. Elvitigala, J. Stöckel, B.K. Ghosh, and H.B. Pakrasis, "Effect of Continuous Light on Diurnal Rhythms in Cyanothece sp. ATCC 51142," BMC Genomics, vol. 10, article no. 226, 2009.
[11] E. Emberly and N.S. Wingreen, "Hourglass Model for a Protein-Based Circadian Oscillator," Physical Rev. Letters, vol. 96, no. 3,article no. 038303, 2006.
[12] S.S. Golden, M. Ishiura, C.H. Johnson, and T. Kondo, "Cyanobacterial Circadian Rhythms," Ann. Rev. Plant Physiology and Plant Molecular Biology, vol. 48, pp. 327-354, 1997.
[13] R. Haselkorn, "Heterocysts," Ann. Rev. Plant Physiology, vol. 29, pp. 319-344, 1978.
[14] M. Ishiura, S. Kutsuna, S. Aoki, H. Iwasaki, C.R. Andersson, A. Tanabe, S.S. Golden, C.H. Johnson, and T. Kondo, "Expression of a Gene Cluster KaiABC as a Circadian Feedback Process in Cyanobacteria," Science, vol. 281, pp. 1519-1523, 1998.
[15] C.H. Johnson, "Circadian Rhythms: As Time Glows by in Bacteria," Nature, vol. 430, pp. 23-24, 2004.
[16] H. Kageyama, T. Kondo, and H. Iwasaki, "Circadian Formation of Clock Protein Complexes by KaiA, KaiB, KaiC, and SasA in Cyanobacteria," J. Biological Chemistry, vol. 278, pp. 2388-2395, 2003.
[17] Y. Kitayama, H. Iwasaki, T. Nishiwaki, and T. Kondo, "KaiB Functions as an Attenuator of KaiC Phosphorylation in the Cyanobacterial Circadian Clock System," The EMBO J., vol. 22, pp. 2127-2134, 2003.
[18] T. Kondo, T. Mori, N.V. Lebedeva, S. Aoki, M. Ishiura, and S.S. Golden, "Circadian Rhythms in Rapidly Dividing Cyanobacteria," Science, vol. 275, pp. 224-227, 1996.
[19] R.E. Kronauer, C.A. Czeisler, S.F. Pilato, M.C. Moore-Ede, and E.D. Weitzman, "Mathematical Model of the Human Circadian System with Two Interacting Oscillators," Am. J. Physiology— Regulatory, Integrative and Comparative Physiology, vol. 242, pp. 3-17, 1982.
[20] Y. Kuramoto, "Self-Entrainment of a Population of Coupled Non-Linear Oscillators," Proc. Int'l Symp. Math. Problems in Theoretical Physics, vol. 39, pp. 420-422, 1975.
[21] Y. Kuramoto, Chemical Oscillations, Waves, and Turbulence. Springer-Verlag, 1984.
[22] G. Kurosawa, K. Aihara, and Y. Iwasa, "A Model for the Circadian Rhythm of Cyanobacteria That Maintains Oscillation without Gene Expression," Biophysical J., vol. 91, pp. 2015-2023, 2006.
[23] Y. Liu, N.F. Tsinoremas, C.H. Johnson, N.V. Lebedeva, S.S. Golden, M. Ishiura, and T. Kondo, "Circadian Orchestration of Gene Expression in Cyanobacteria," Genes and Development, vol. 9, pp. 1469-1478, 1995.
[24] A. Mehra, C.I. Hong, M. Shi, J.J. Loros, J.C. Dunlap, and P. Ruoff, "Circadian Rhythmicity by Autocatalysis," PLos Computational Biology, vol. 2, no. 7, pp. 816-823, 2006.
[25] F. Miyoshi, Y. Nakayama, K. Kaizu, H. Iwasaki, and M. Tomita, "A Mathematical Model for the Kai-Protein-Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria," J. Biological Rhythms, vol. 22, pp. 69-80, 2007.
[26] T. Mori, B. Binder, and C.H. Johnson, "Circadian Gating of Cell Division in Cyanobacteria Growing with Average Doubling Times of Less Than 24 Hours," Proc. Nat'l Academy of Sciences USA, vol. 93, pp. 10183-10188, 1996.
[27] F. Naef, "Circadian Clocks Go In Vitro: Purely Post-Translational Oscillators in Cyanobacteria," Molecular Systems Biology, vol. 1, article no. 2005.0019, 2005.
[28] Y. Nakahira, M. Katayama, H. Miyashita, S. Kutsuna, H. Iwasaki, T. Oyama, and T. Kondo, "Global Gene Repression by KaiC as a Master Process of Prokaryotic Circadian System," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 881-885, 2004.
[29] M. Nakajima, K. Imai, H. Ito, T. Nishiwaki, Y. Murayama, H. Iwasaki, T. Oyama, and T. Kondo, "Reconstitution of Circadian Oscillation of Cyanobacterial KaiC Phosphorylation in Vitro," Science, vol. 308, pp. 414-415, 2005.
[30] T. Nishiwaki, Y. Satomi, M. Nakajima, C. Lee, R. Kiyohara, H. Kageyama, Y. Kitayama, M. Temamoto, A. Yamaguchi, A. Hijikata, M. Go, H. Iwasaki, T. Takao, and T. Kondo, "Role of KaiC Phosphorylation in the Circadian Clock System of Synechococcus elongatus PCC 7942," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 13927-13932, 2004.
[31] K. Onai, M. Morishita, S. Itoh, K. Okamoto, and M. Ishiura, "Circadian Rhythms in the Thermophilic Cyanobacterium Thermosynechococcus Elongatus: Compensation of Period Length over a Wide Temperature Range," J. Bacteriology, vol. 186, no. 15, pp. 4972-4977, 2004.
[32] J. Quackenbush, "Microarray Data Normalization and Transformation," Nature Genetics, vol. 32, pp. 496-501, 2002.
[33] R.J. Reddy, J.B. Haskell, D.M. Sherman, and L.A. Sherman, "Unicellular, Aerobic Nitrogen-Fixing Cyanobacteria of the Genus Cyanothece," J. Bacteriology, vol. 175, pp. 1284-1292, 1993.
[34] S.M. Reppert and D.R. Weaver, "Coordination of Circadian Timing in Mammals," Nature, vol. 418, pp. 935-941, 2002.
[35] A. Sehgal, Molecular Biology of Circadian Rhythms. John Wiley & Sons, Inc., 2004.
[36] P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker, "Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks," Genome Research, vol. 13, pp. 2498-2504, 2003.
[37] L.A. Sherman, P. Meunier, and M.S. Colon-Lopez, "Diurnal Rhythms in Metabolism: A Day in the Life of a Unicellular, Diazotrophic Cyanobacterium," Photosynthesis Research, vol. 58, pp. 25-42, 1998.
[38] J. Stöckel, E.A. Welsh, M. Liberton, R. Kunnavakkam, R. Aurora, and H.B. Pakrasi, "Global Transcriptomic Analysis of Cyanothece 51142 Reveals Robust Diurnal Oscillation of Central Metabolic Processes," Proc. Nat'l Academy of Sciences USA, vol. 105, pp. 6156-6161, 2008.
[39] S.H. Strogatz and I. Stewart, "Coupled Oscillators and Biological Synchronization," Scientific Am., vol. 269, pp. 102-109, 1993.
[40] J. Toepel, E. Welsh, T.C. Summerfield, H.B. Pakrasi, and L.A. Sherman, "Differential Transcriptional Analysis of the Cyanobacterium Cyanothece sp. Strain ATCC 51142 during Light-Dark and Continuous-Light Growth," J. Bacteriology, vol. 190, pp. 3904-3913, 2008.
[41] J.J. Tyson, C.I. Hong, C.D. Thron, and B. Novak, "A Simple Model of Circadian Rhythms Based on Dimerization and Proteolysis of Per and Tim," Biophysical J., vol. 77, pp. 2411-2417, 1999.
[42] A.T. Winfree, The Geometry of Biological Time. Springer, 1980.
[43] C.P. Wolk, "Heterocyst Formation," Ann. Rev. Genetics, vol. 30, pp. 59-78, 1996.
[44] M.W. Young and S.A. Kay, "Time Zones: A Comparative Genetics of Circadian Clocks," Nature Rev. Genetics, vol. 2, pp. 702-715, 2001.
447 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool