Preferences help
enabled [disable] Abstract
Number of results
2006 | 53 | 1 | 1-10
Article title

Regulatory mechanisms of gene expression: complexity with elements of deterministic chaos

Title variants
Languages of publication
Linear models based on proportionality between variables have been commonly applied in biology and medicine but in many cases they do not describe correctly the complex relationships of living organisms and now are being replaced by nonlinear theories of deterministic chaos. Recent advances in molecular biology and genome sequencing may lead to a simplistic view that all life processes in a cell, or in the whole organism, are strictly and in a linear fashion controlled by genes. In reality, the existing phenotype arises from a complex interaction of the genome and various environmental factors. Regulation of gene expression in the animal organism occurs at the level of epigenetic DNA modification, RNA transcription, mRNA translation, and many additional alterations of nascent proteins. The process of transcription is highly complicated and includes hundreds of transcription factors, enhancers and silencers, as well as various species of low molecular mass RNAs. In addition, alternative splicing or mRNA editing can generate a family of polypeptides from a single gene. Rearrangement of coding DNA sequences during somatic recombination is the source of great variability in the structure of immunoglobulins and some other proteins. The process of rearrangement of immunoglobulin genes, or such phenomena as parental imprinting of some genes, appear to occur in a random fashion. Therefore, it seems that the mechanism of genetic information flow from DNA to mature proteins does not fit the category of linear relationship based on simple reductionism or hard determinism but would be probably better described by nonlinear models, such as deterministic chaos.
Physical description
  • Department of Cellular Biochemistry, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland
  • Department of Cellular Biochemistry, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland
  • Department of Animal Reproduction, National Research Institute of Animal Production, Balice, Poland
  • Department of Cellular Biochemistry, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland
  • Akira S, Okazaki K, Sakano H (1987) Two pairs of recombination signals are sufficient to cause immunoglobulin V-(D)-J joining. Science 238: 1134-1138.
  • Barbon A, Vallini I, La Via L, Marchina E, Barlati S (2003) Glutamate receptor RNA editing: a molecular analysis of GluR2, GluR5 and GluR6 in human brain tissues and in NT2 cells following in vitro neural differentiation. Brain Res Mol Brain Res 117: 168-178.
  • Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10: 211-219.
  • Brannan CL, Bartolomei MS (1999) Mechanism of genomic imprinting. Curr Opin Genet Dev 9: 164-170.
  • Brennan SO (1989) Propeptide cleavage: evidence from human proalbumins. Mol Biol Med 6: 87-92.
  • Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HF (1992) The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542.
  • Cawthon RM, Andersen LB, Buchberg AM, Xu GF, O'Connell P, Viskochil D, Weiss RB, Wallace MR, Marchuk DA, Culver M, et al. (1991) cDNA sequence and genomic structure of EV12B, a gene lying within an intron of the neurofibromatosis type 1 gene. Genomics 9: 446-460.
  • Chambeyron S, Bickmore WA (2004) Does looping and clustering in the nucleus regulate gene expression? Curr Opin Cell Biol 16: 256-262.
  • Chelly J, Kaplan JC, Maire P, Gautron S, Kahn A (1988) Transcription of the dystrophin gene in human muscle and non-muscle tissue. Nature 333: 858-860.
  • Chelly J, Concordet JP, Kaplan JC, Kahn A (1989) Illegitimate transcription: transcription of any gene in any cell type. Proc Natl Acad Sci USA 86: 2617-2621.
  • Chess A, Simon I, Cedar H, Axel R (1994) Allelic inactivation regulates olfactory receptor gene expression. Cell 78: 823-834.
  • Chorazy M (2005) Is gene concept facing dethronisation? Folia Histochem Cytobiol (Suppl 1) 43: 9.
  • Chow JC, Brown CJ (2003) Forming facultative heterochromatin: silencing of an X chromosome in mammalian females. Cell Mol Life Sci 60: 2586-2603.
  • Claverie JM (2001) Gene number. What if there are only 30,000 human genes? Science 291: 1255-1257.
  • Cooper TA (2002) mRNA splicing: regulated and differential. In Encyclopedia of Life Sciences,
  • Couzin J (2002) Cell biology. Chaos reigns in RNA transcription. Science 298: 1538.
  • Cox GF, Kunkel LM (1997) Dystrophies and heart disease. Curr Opin Cardiol 12: 329-343.
  • Croft L, Schandorff S, Clark F, Burrage K, Arctander P, Mattick JS (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet 24: 340-341.
  • Driscoll DM, Wynne JK, Wallis SC, Scott J (1989) An in vitro system for the editing of apolipoprotein B mRNA. Cell 58: 519-525.
  • Fugmann SD, Lee AI, Shockett PE, Villey IJ, Schatz DG (2000) The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu Rev Immunol 18: 495-527.
  • Hastie ND, Bishop JO (1976) The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9: 761-774.
  • Higgins JP (2002) Nonlinear systems in medicine. Yale J Biol Med 75: 247-260.
  • Hook V, Yasothornsrikul S, Greenbaum D, Medzihradszky KF, Troutner K, Toneff T, Bundey R, Logrinova A, Reinheckel T, Peters C, Bogyo M (2004) Cathepsin L and Arg/Lys aminopeptidase: a distinct prohormone processing pathway for the biosynthesis of peptide neurotransmitters and hormones. Biol Chem 385: 473-480.
  • Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O'Hare MJ, Neville AM, Simpson AJ, Strausberg RL (2003) Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci USA 100: 4702-4705.
  • Jones PA, Laird PW (1999) Cancer epigenetics comes of age. Nat Genet 21: 163-167.
  • Jurka J (2004) Evolutionary impact of human Alu repetitive elements. Curr Opin Genet Dev 14: 603-8.
  • Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. Plos Biol doi: 10.1371
  • Koj A, Dubin A, Kasperczyk H, Bereta J, Gordon AH (1982) Changes in blood level and affinity to concanavalin A of rat plasma glycoproteins during acute inflammation and hepatoma growth. Biochem J 206: 545-553.
  • Korn H, Faure P (2003) Is there chaos in the brain ? Experimental evidence and related models. C R Biol 326: 787-840.
  • Laity JH, Dyson HJ, Wright PE (2000) Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein. Proc Natl Acad Sci USA 97: 11932-11935.
  • Larsson SH, Charlieu JP, Miyagawa K, Engelkamp D, Rassoulzadegan M, Ross A, Cuzin F, van Heyningen V, Hastie ND (1995) Subnuclear localization of WT1 in splicing or transcription factor domains is regulated by alternative splicing. Cell 81: 391-401.
  • Ledbetter DH, Riccardi VM, Airhart SD, Strobel RJ, Keenan BS, Crawford JD (1981) Deletions of chromosome 15 as a cause of the Prader-Willi syndrome. N Engl J Med 304: 325-329.
  • Lefebvre JH, Goodings DA, Kamath MV, Fallen EL (1993) Predictability of normal heart rhythms and deterministic chaos. Chaos 3: 267-276.
  • Levinson B, Kenwrick S, Gamel P, Fisher K, Gitschier J (1992) Evidence for a third transcript from the human factor VIII gene. Genomics 14: 585-589.
  • Lopez AJ (1998) Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet 32: 279-305.
  • Lu B (2003) Pro-region of neurotrophins: role in synaptic modulation. Neuron 39: 735-738.
  • Lyon MF (1999) X-chromosome inactivation. Curr Biol 9: R235-7.
  • Matlin AJ, Clark F, Smith CWJ (2005) Understanding alternative splicing: towards a cellular code. Nature 6: 386-398.
  • Maynard Smith J (2001) Evolution and information. In Images of the World - Science, Humanities, Art (Koj A, Sztompka P, eds) pp 13-17, Uniwersytet Jagiellonski, Krakow.
  • McGrath J, Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37: 179-183.
  • Misteli T (2005) Concepts in nuclear architecture. Bioessays 27: 477-487.
  • Morowitz HJ (2002) The Emergence of Everything, Oxford University Press.
  • Mostoslavsky R, Singh N, Tenzen T, Goldmit M, Gabay C, Elizur S, Qi P, Reubinoff BE, Chess A, Cedar H, Bergman Y (2001) Asynchronous replication and allelic exclusion in the immune system. Nature 414: 221-225.
  • Muc-Wierzgon M, Nowakowska-Zajdel E, Kokot T, Sosada K, Zubelewicz B, Wierzgon J, Cichocka M, Fatyga E, Brodziak A (2004) On the holistic approach in cancer biology: tumor necrosis factor, colon cancer cells, chaos theory and complexity. J Biol Regul Homeost Agents 18: 261-267.
  • Oettinger MA, Schatz DG, Gorka C, Baltimore D (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517-1523.
  • Ohta T (2005) Gene families, multigene families and superfamilies. Nature Encyclopedia of the Human Genome,
  • Parada LA, McQueen PG, Misteli T (2004) Tissue-specific spatial organization of genomes. Genome Biol 5: R44.
  • Paszewski A (2005) What is determined and and what random in biological systems - when does freedom begin? Nauka 1: 53-66 (in Polish).
  • Prank K, Harms H, Brabant G, Hesch RD, Dammig M, Mitschke F (1995) Nonlinear dynamics in pulsatile secretion of parathyroid hormone in normal human subjects. Chaos 5: 76-81.
  • Prusiner SB (1998) Prions. Proc Natl Acad Sci USA 95: 13363-13383.
  • Ragoczy T, Telling A, Sawado T, Groudine M, Kosak ST (2003) A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res 11: 513-525.
  • Reik W, Walter J (1998) Imprinting mechanisms in mammals. Curr Opin Genet Dev 8: 154-164.
  • Sakano H, Huppi K, Heinrich G, Tonegawa S (1979) Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280: 288-294.
  • Savageau MA (2001) Design principles for elementary gene circuits: elements, methods and examples. Chaos 11: 142-159.
  • Schatz DG, Oettinger MA, Baltimore D (1989) The V(D)J recombination activating gene, RAG-1. Cell 59: 1035-1048.
  • Sharma PM, Bowman M, Madden SL, Rauscher FJ 3rd, Sukumar S (1994) RNA editing in the Wilms' tumor susceptibility gene, WT1. Genes Dev 8: 720-731.
  • Shmulevich I, Kauffman SA, Aldana M (2005) Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc Natl Acad Sci USA 102: 13439-13444.
  • Skok JA, Brown KE, Azuara V, Caparros ML, Baxter J, Takacs K, Dillon N, Gray D, Perry RP, Merkenschlager M, Fisher AG (2001) Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat Immunol 2: 848-854.
  • Surani MAH, Barton SC, Norris ML (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308: 548-550.
  • Surani MAH, Barton SC, Norris ML (1986). Nuclear transplantation in the mouse: heritable differences between parental genomes after activation of the embryonic genome. Cell 45: 127-136.
  • Szymanski M, Barciszewski J (2003) Regulation by RNA. Int Rev Cytol 231: 197-258.
  • Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575-581.
  • Van Dijk W, Mackiewicz A (1993) Control of glycosylation alterations of acute phase glycoproteins. In Acute Phase Proteins (Mackiewicz A, Kushner I, Baumann H, eds) pp 559-580, CRC Press, Boca Raton, Ann Arbor, London, Tokyo.
  • Vega IE, Cui L, Propst JA, Hutton ML, Lee G, Yen SH (2005) Increase in tau tyrosine phosphorylation correlates with the formation of tau aggregates. Brain Res Mol Brain Res 138: 135-144.
  • Watson JD, Crick FHC (1953) Molecular structure of nucleic acids. Nature 171: 737-738.
Document Type
Publication order reference
YADDA identifier
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.