Skip to main content
SpringerLink
Log in

The multiple codes of nucleotide sequences

  • Viewpoint
  • Published:
Bulletin of Mathematical Biology Aims and scope Submit manuscript

Abstract

Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). Several codes of nucleotide sequences are discussed including: (1) the translation framing code, responsible for correct triplet counting by the ribosome during protein synthesis; (2) the chromatin code, which provides instructions on appropriate placement of nucleosomes along the DNA molecules and their spatial arrangement; (3) a putative loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. Tandemly repeated sequences frequently considered as functionless “junk” are found to be grouped into certain classes of repeat unit lengths. This indicates some functional involvement of these sequences. A hypothesis is formulated according to which the tandem repeats are given the role of weak enhancer-silencers that modulate, in a copy number-dependent way, the expression of proximal genes. Fast amplification and elimination of the repeats provides an attractive mechanism of species adaptation to a rapidly changing environment.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Literature

  • Arques, D. G. and C. J. Michel. 1987. “A Purine-Pyrimidine Motif Verifying an Identical Presence in Almost All Gene Taxonomic Groups,”J. theor. Biol.,128, 457–461.

    Google Scholar 

  • Atkins, J. F., D. Elseviers and L. Gorini. 1972. “Low Activity of Beta-Galactosidase in Frameshift Mutants ofEscherichia coli.”Proc. natl. Acad. Sci. U.S.A.,69, 1192–1195.

    Article  Google Scholar 

  • Beckmann, J. S., V. Brendel and E. N. Trifonov. 1986. “Intervening Sequences Exhibit Distinct Vocabulary.”J. Biomolec. Struct. Dynamics,4, 391–400.

    Google Scholar 

  • Bernardi, G., B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival and F. Rodier. 1985. “The Mosaic Genome of Warm-Blooded Vertebrates.”Science 228, 953–957.

    Google Scholar 

  • Blaisdell, B. E., 1983. “A Prevalent, Persistent Global Nonrandomness that Distinguishes Coding and Non-Coding Eukaryotic Nuclear DNA Sequences.”J. molec. Evol.,19, 122–133.

    Article  Google Scholar 

  • Breathnach, R. and P. Chambon. 1981. “Organization and Expression of Eucaryotic Split Genes Coding for Proteins.”Ann. Rev. Biochem. 50, 349–383.

    Article  Google Scholar 

  • Brendel, V., J. S. Beckmann and E. N. Trifonov. 1986. “Linguistics of Nucleotide Sequences: Morphology and Comparison of Vocabularies.”J. Biomolec. Struct. Dynamics 4, 11–21.

    Google Scholar 

  • Bullock, P., J. Miller and M. Botchan. 1986. “Effects of Poly{d(pGpT)·d(pApC)} and Poly}d(pCpG)·d(pCpG)} Repeats on Homologous Recombination in Somatic Cells.”Molec. Cell. Biol. 6, 3948–3953.

    Google Scholar 

  • Claverie, J.-M. and L. Bougueleret. 1986. “Heuristic Informational Analysis of Sequences.”Nucl. Acids Res.,14, 179–196.

    Google Scholar 

  • Cold Spring Harbour Symp. Quant. Biol. 42, Pt. 1. 1977.

  • Craigen, W. J. and T. Caskey. 1986. “Expression of Peptide, Chain Release Factor 2 Requires High-Efficiency Frameshift.”Nature 322, 273–275.

    Article  Google Scholar 

  • Doolittle, W. F. and C. Sapienza. 1980. “Selfish Genes, the Phenotype Paradigm and Genome Evolution.”Nature 284, 601–603.

    Article  Google Scholar 

  • Dover, G. 1980. “Ignorant DNA?”Nature 285, 618–620.

    Article  Google Scholar 

  • Eisenberg, D. S., R. M. Weiss and T. C. Terwilliger. 1984. “The Hydrophobic Moment Detects Periodicity In Protein Hydrophobicity.”Proc. natl Acad. Sci. U.S.A. 81, 140–144.

    Article  Google Scholar 

  • Galas, D. J., M. Eggert and M. S. Waterman. 1985. “Rigorous Pattern-Recognition Methods for DNA Sequences. Analysis of Promoter Sequences fromEscherichia coli.”J. molec. Biol. 186, 117–128.

    Article  Google Scholar 

  • Goldberg, M. 1979. Ph.D. thesis, Stanford University, Stanford, CA.

    Google Scholar 

  • Godson, B. R., B. G. Barrell, R. Staden and J. C. Fiddes. 1978. “Nucleotide Sequence of Bacteriophage G4 DNA.”Nature 276, 236–247.

    Article  Google Scholar 

  • Griffith, J., M. Bleyman, C. A. Rauch, P. A. Kitchin and P. T. Englund. 1986. “Visualization of the Bent Helix in Kinetoplast DNA by Electron Microscopy.”Cell 46, 717–724.

    Article  Google Scholar 

  • Hamada, H., M. Seidman, B. H. Howard and C. M. Gorman. 1984. “Enhanced Gene Expression by the Poly(dT-dG)·poly(dC-dA) Sequence.”Molec. Cell. Biol.,4, 2622–2630.

    Google Scholar 

  • Harris, Z. 1955. “From Phoneme to Morpheme.”Language 31, 190–222.

    Article  Google Scholar 

  • Hsieh, C.-H. and J. D. Griffith. 1988. “The Terminus of SV40 DNA Replication and Transcription Contains a Sharp Sequence-Directed Curve.Cell 52, 535–544.

    Article  Google Scholar 

  • Karlin, S. and G. Ghandour. 1985. “The Use of Multiple Alphabets in Kappa-Gene Immunoglobulin DNA Sequence Comparisons.”EMBO J. 4, 1217–1223.

    Google Scholar 

  • Konopka, K. L., J. Reiter, M. Jung, D. A. Zarling and T. M. Jovin. 1985. “Concordance of Experimentally Mapped or Predicted Z-DNA Sites with Positions of Selected Alternating Purine-Pyrimidine Tracts.”Nucl. Acids Res. 13, 1683–1701.

    Google Scholar 

  • Kozak, M. 1987. “An Analysis of 5′-Noncoding Sequences from 699 Vertebrate Messenger RNAs.”Nucl. Acids Res. 15, 8125–8148.

    Google Scholar 

  • Marini, J. C., S. D. Levene, D. M. Crothers and P. T. Engluind. 1982. “Bent Helical Structure in Kinetoplast DNA.”Proc. natl. Acad. Sci. U.S.A. 79, 7664–7668.

    Article  Google Scholar 

  • Maxam, A. and W. Gilbert. 1980. “Sequencing End-Labeled DNA with Base Specific Chemical Cleavages.”Meth. Enzymol. 65, 499–560.

    Google Scholar 

  • Mazrimas, J. A. and F. T. Hatch. 1972. “A Possible Relationship Between Satellite DNA and the Evolution of Kangaroo rat Species (GenusDipodomys)”Nature, New Biol. 240, 102–105.

    Article  Google Scholar 

  • Mengeritsky, G. and E. N. Trifonov. 1983. “Nucleotide Sequence-directed Mapping of the Nucleosomes.”Nucl. Acids Res. 11, 3833–3851.

    Google Scholar 

  • Miklos, G. L. G. 1985. “Localized Highly Repetitive DNA Sequences in Vertebrate and Invertebrate Genomes.” InMolecular Evolutionary Genetics, R. J. MacIntyre (Ed.), pp. 241–321. New York: Plenum Press.

    Google Scholar 

  • Mirkin, S. M., V. I. Lyamichev, K. N. Drushlyak, V. N. Dobrynin, S. A. Filippov and M. D. Frank-Kamenetskii. 1987. “DNA H Form Requires a Homopurine-Homopyrimidine Mirror Repeat.”Nature 330, 495–497.

    Article  Google Scholar 

  • Nirenberg, M. W., O. W. Jones, P. Leder, B. F. C. Clark, W. S. Sly and S. Pestka. 1963. “On the Coding of Genetic Information.”Cold Spring Harbour Symp. Quant. Biol.,28, 549–557.

    Google Scholar 

  • Noll, M., S. Zimmer, A. Engel and J. Dubochet. 1980. “Self-Assembly of Single and Closely Spaced Nucleosome Core Particles.”Nucl. Acids. Res. 8, 21–42.

    Google Scholar 

  • Normark, S., S. Bergstrom, T. Edlund, T. Grundstrom, B. Jaurin, F. P. Lindberg and O. Olsson. 1983. “Overlapping Genes”Ann. Rev. Genet. 17, 499–525.

    Article  Google Scholar 

  • Nucleotide Sequences 1987. A Compilation from the GenBank and EMBL Data Libraries. 1987. Washington: IRL Press.

  • Ohno, S. 1970. “So Much ‘Junk’ DNA in Our Genome.” InEvolution of Genetic Systems, Vol. 23, H. H. Smith (Ed.), pp. 366–370. New York: Gordon and Breach.

    Google Scholar 

  • Ohshima, Y. and Y. Gotoh. 1987. “Signals for the Selection of a Splice Site in pre-mRNA. Computer Analysis of Splice Junction Sequences and Like Sequences.”J. molec. Biol. 195, 247–259.

    Article  Google Scholar 

  • Olson, W. K., M. H. Sarma, R. H. Sarma and M. Sundaralingam (Eds). 1988.Structure and Expression. Vol. 3: DNA Bending and Curvature. New York: Adenine Press.

    Google Scholar 

  • Orgel, L. E. and F. H. C. Crick. 1980. “Selfish DNA: the Ultimate Parasite.”Nature,284, 604–607.

    Article  Google Scholar 

  • Peterson, R. C., J. L. Doering and D. D. Brown. 1980. “Characterization of Two Xenopus Somatic 5S DNAs and One Minor Oocyte-Specific 5S DNA.”Cell 20, 131–141.

    Article  Google Scholar 

  • Pribnow, D. 1979. “Genetic Control Signals in DNA.” InBiological Regulation and Development, R. F. Goldberger (Ed.), pp. 219–278. New York: Plenum Press.

    Google Scholar 

  • Proudfoot, N. and G. G. Brownlee. 1976. “3′ Non-coding Region Sequences in Eukaryotic Messenger RNA.”Nature 263, 211–214.

    Article  Google Scholar 

  • Reddy, V. B., B. Thimmappaya, R. Dhar, K. N. Subramanian, B. S. Zain, J. Pan, P. K. Ghosh, M. L. Celma and S. M. Weissman. 1978. “The Genome of Simian Virus 40.”Science 200, 494–502.

    Google Scholar 

  • Sanger, F., S. Nicklen and A. R. Coulson. 1977. “DNA Sequencing with Chain-terminating Inhibitors.”Proc. natn. Acad. Sci. U.S.A. 74 5463–5467.

    Article  Google Scholar 

  • Satchwell, S. C., H. R. Drew and A. A. Travers. 1986. “Sequence Periodicities in Chicken Nucleosome Core DNA.”J. molec. Biol.,191, 659–675.

    Article  Google Scholar 

  • Sharp, P. A. 1987. “Splicing of Messenger RNA Precursors.”Science 235 766–771.

    Google Scholar 

  • Singer, M. F. 1982. “Highly Repeated Sequences in Mammalian Genomes.”Int. Rev. Cytol. 76, 67–112.

    Article  Google Scholar 

  • Speyer, J. F., P. Lengyel, C. Basilio, A. J. Wahba, R. S. Gardner and S. Ochoa 1963. “Synthetic Polynucleotides and Amino Acid Code.”Cold Spr. Harbour Symp. Quant. Biol. 28, 559–567.

    Google Scholar 

  • Thoma, F., L. W. Bergman and R. T. Simpson. 1984. “Nuclease Digestion of Circular TRP1ARS1 Chromatin Reveals Positioned Nucleosomes Separated by Nuclease-Sensitive Regions.”J. molec. Biol. 177, 715–733.

    Article  Google Scholar 

  • Trifonov, E. N. 1980. “Sequence-Dependent Deformational Anisotropy of Chromatin DNA.”Nucl. Acids. Res. 8, 4041–4053.

    Google Scholar 

  • —. 1983a. “Nucleosomal DNA Structure.” InNucleic Acids: The Vectors of Life, B. Pullman and J. Jortner (Eds), pp. 373–385. Dordrecht: Reidel.

    Google Scholar 

  • —. 1983b. “Sequence-Dependent Variations of B-DNA Structure and Protein-DNA Recognition.”Cold Spring Harbour Symp. Quant. Biol. 47, 271–278.

    Google Scholar 

  • — 1984. “Construction of an Algorithm for Locating Splicing Junctions.”CODATA Bull. 56, 17–20.

    Google Scholar 

  • — 1987. “Translation Framing Code and Frame-Monitoring Mechanism as Suggested by the Analysis of mRNA and 16S rRNA Nucleotide Sequences.”J. molec. Biol. 194, 643–652.

    Article  Google Scholar 

  • — and V. Brendel. 1986.Gnomic—A Dictionary of Genetic Codes. Rehovot, PA: Balaban.

    Google Scholar 

  • Trifonov, E. N. and V. Brendel.Gnomic—a Dictionary of Genetic Codes (2nd Edn). Verlag Chemie, in preparation.

  • — and G. Mengeritsky. 1988. “Bent DNA in Chromatin Versus Free Curved DNA.” InStructure and Expression. Vol. 3: DNA Bending and Curvature, W. K. Olson, M. H. Sarma, R. H. Sarma and M. Sundaralingam (Eds), pp. 159–167. New York: Adenine Press.

    Google Scholar 

  • — and J. L. Sussman. 1980. “The Pitch of Chromatin DNA is Reflected in its Nucleotide Sequence.”Proc. natl Acad. Sci. U.S.A. 77, 3816–3820.

    Article  Google Scholar 

  • — and L. E. Ulanovsky. 1987. “Inherently Curved DNA and its Structural Elements.” InUnusual DNA Structures, R. D. Wells and S. C. Harvey (Eds), pp. 173–187. New York: Springer.

    Google Scholar 

  • Tschumper, G. and J. Carbon. 1980. “Sequence of a Yeast DNA Fragment Containing a Chromosomal Replicator and the TRP1 Gene.”Gene 10, 157–166.

    Article  Google Scholar 

  • Ulanovsky, L. E., M. Bodner, E. N. Trifonov and M. Choder. 1986. “Curved DNA: Design, Synthesis and Circularization.”Proc. natl Acad. Sci. U.S.A. 83, 862–866.

    Article  Google Scholar 

  • — and E. N. Trifonov. 1986. “A Different View Point on the Chromatin High Order Structure: Steric Exclusion Effects.” InBiomolecular Stereodynamics III, R. H. Sarma and M. H. Sarma (Eds), pp. 35–44. New York: Adenine Press.

    Google Scholar 

  • — and —. 1987. “Estimation of Wedge Components in Curved DNA.”Nature 326, 720–722.

    Article  Google Scholar 

  • von Heijne, G. 1987.Sequence Analysis in Molecular Biology—Treasure Trove or Trivial Pursuit. New York: Academic Press.

    Google Scholar 

  • Watanabe, S. and K. Yoshiike. 1985. “Decreasing the Number of 68-base-pair Tandem Repeats in the BK Virus Transcriptional Control Region Reduces Plaque Size and Enhances Transforming Capacity.”J. Virol.55, 823–825.

    Google Scholar 

  • Wei, R., H. Wilkinson, K. Pfeifer, C. Schneider, R. Young and L. Guarente. 1986. “Two or More Copies of Drosophila Heat Shock Consensus Sequence Serve to Activate Transcription in Yeast.”Nucl. Acids Res. 14, 8183–8188.

    Google Scholar 

  • Weiss, R. B., D. M. Dunn, A. E. Dahlberg, J. F. Atkins and R. F. Gesteland. 1988. “Reading Frame Switch Caused by Base-Pair Formation Between the 3′-End of 16S rRNA and the mRNA During Elongation of Protein Synthesis inEscherichia coli.”EMBO J. 7, 1503–1507.

    Google Scholar 

  • Zhang, K., W. F. Bosron and H. J. Edenberg. 1987. “Structure of the Mouse Adh-1 Gene and identification of a Deletion in a Long Alternating Purino-Pyrimidine Sequence in the First Intron of Strains Expressing Low Alcohol Dehydrogenase Activity.”Gene 57, 27–36.

    Article  Google Scholar 

  • Zuckerkandl, E. 1986. “Polite DNA: Functional Density and Functional Compatibility in Genomes.”J. molec. Evol. 24, 12–27.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Polymer Research, The Weizmann Institute of Science, 76100, Rehovot, Israel

    E. N. Trifonov

Authors
  1. E. N. Trifonov
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Trifonov, E.N. The multiple codes of nucleotide sequences. Bltn Mathcal Biology 51, 417–432 (1989). https://doi.org/10.1007/BF02460081

Download citation

  • Received:

  • Revised:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02460081

Keywords

Search

Navigation