Skip to main content
SpringerLink
Log in

Segmented Genome: Elementary Units of Genome Structure

  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Numerous observations, measurements and calculations strongly indicate that both eukaryotic and prokaryotic genomes are built as linear arrays of units of rather uniform size, about 400 base pairs. The units are likely to correspond to early individual genes that existed, presumably, in form of DNA circles. Their combinatorial fusion resulted eventually in formation of the early segmented genomes. The segmented structure of the genomes is, apparently, still maintained by some structural selection pressures. Some of the units can be recognized by characteristic sequence motifs at the borders of the units. Identification and characterization of the units, their mapping on the genomes should become an important prerequisite of genome comparisons and genome evolution studies.

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

REFERENCES

  1. Riesner, D., Steger, G., Schumacher, J., et al., Structure and Function of Viroids, Biophys. Struct. Mech., 1983, vol. 9, pp. 145-170.

    Google Scholar 

  2. Trifonov, E.N., Segmented Structure of Protein Sequences and Early Evolution of Genome by Combinatorial Fusion of DNA Elements, J. Mol. Evol., 1995, vol. 40, pp. 337-342.

    Google Scholar 

  3. Berezovsky, I.N. and Trifonov, E.N., Evolutionary Aspects of Protein Structure and Folding, Mol. Biol., 2001, vol. 35, pp. 233-239.

    Google Scholar 

  4. Trifonov, E.N., Kirzhner, A., Kirzhner, V.M., and Berezovsky, I.N., Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis, J. Mol. Evol., 2001, vol. 53, pp. 394-401.

    Google Scholar 

  5. Yamakawa, H. and Stockmeyer, W.H., Statistical Mechanics of Wormlike Chains: II. Excluded Volume Effects, J. Chem. Phys., 1972, vol. 57, pp. 2843-2854.

    Google Scholar 

  6. Shimada, J. and Yamakawa, H., Ring-Closure Probabilities for Twisted Worm-like Chains. Application to DNA, Macromolecules, 1984, vol. 17, pp. 689-698.

    Google Scholar 

  7. Berezovsky, I.N., Grosberg, A.Y., and Trifonov, E.N., Closed Loops of Nearly Standard Size: Common Basic Element of Protein Structure, FEBS Lett., 2000, vol. 466, pp. 283-286.

    Google Scholar 

  8. Shore, D., Langowski, J., and Baldwin, R.L., DNA Flexibility Studied by Covalent Closure of Short Fragments into Circles, Proc. Natl. Acad. Sci. USA, 1981, vol. 78, pp. 4833-4837.

    Google Scholar 

  9. Jones, S., Stewart, M., Michie, A., et al., Domain Assignment for Protein Structures Using a Consensus Approach: Characterization and Analysis, Protein Sci., 1998, vol. 7, pp. 233-242.

    Google Scholar 

  10. Wheelan, S.J., Marchler-Bauer, A., and Bryant, S.H., Domain Size Distribution Can Predict Domain Boundaries, Bioinformatics, 2000, vol. 16, pp. 613-618.

    Google Scholar 

  11. Svedberg, T., Mass and Size of Protein Molecules, Nature, 1929, vol. 123, p. 871.

    Google Scholar 

  12. Svedberg, T., The Ultra-Centrifuge and the Study of High-Molecular Compounds, Nature, 1937, vol. 139, pp. 1051-1062.

    Google Scholar 

  13. Goryshin, I.Y., Kil, Y.V., and Reznikoff, W.S., DNA Length, Bending, and Twisting Constraints on IS50 Transposition, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 10834-10838.

    Google Scholar 

  14. Trifonov, E.N., Segmented Structure of Mobile and Separate DNA and RNA Elements as Suggested by Their Size Distributions, J. Biomol. Struct. Dyn., 1997, vol. 14, pp. 449-457.

    Google Scholar 

  15. Hewish, D.R. and Burgoyne, L.A., Chromatin Substructure: The Digestion of Chromatin DNA at Regularly Spaced Sites by a Nuclear Deoxyribonuclease, Biochem. Biophys. Res. Commun., 1973, vol. 52, pp. 504-510.

    Google Scholar 

  16. Van Holde, K.E., Chromatin, New York: Springer Verlag, 1988.

    Google Scholar 

  17. Burgoyne, L.A. and Skinner, J.D., Chromatin Super-structure: the Next Level of Structure above the Nucleosome Has an Alternating Character. A Two-Nucleosome Based Series Is Generated by Probes Armed with DNase-I Acting on Isolated Nuclei, Biochem. Biophys. Res. Commun., 1981, vol. 99, pp. 893-899.

    Google Scholar 

  18. Khachatrian, A.T., Pospelov, V.A., Svetlikova, S.B., and Vorobiev, V.I., Nucleodisome-a New Repeat Unit of Chromatin Revealed in Nuclei of Pigeon Erythrocytes by DNase I Digestion, FEBS Lett., 1981, vol. 128, pp. 90-92.

    Google Scholar 

  19. Wada-Kiyama, Y. and Kiyama, R., Conservation and Periodicity of DNA Bend Sites in the Human Beta-Globin Gene Locus, J. Biol. Chem., 1995, vol. 270, pp. 12439-12445.

    Google Scholar 

  20. Wada-Kiyama, Y. and Kiyama, R., Conservation and Periodicity of DNA Bend Sites in Eukaryotic Genomes, DNA Res., 1996, vol. 3, pp. 25-30.

    Google Scholar 

  21. Savageau, M.A., Proteins of Escherichia coli Come in Sizes That Are Multiples of 14 kDa: Domain Concepts and Evolutionary Implications, Proc. Natl. Acad. Sci. USA, 1986, vol. 83, pp. 1198-1202.

    Google Scholar 

  22. Berman, A.L., Kolker, E., and Trifonov, E.N., Underlying Order in Protein Sequence Organization, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 4044-4047.

    Google Scholar 

  23. Kolker, E., Tjaden, B., Hubley, R., et al., Spectral Analysis of Distributions: Finding Periodic Components in Eukaryotic Enzyme Length Data, OMICS J. Integr. Biol. (in press).

  24. Kolker, E. and Trifonov, E.N., Periodic Recurrence of Methionines: Fossil of Gene Fusion?, Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 557-560.

    Google Scholar 

  25. Krasheninnikov, I.A., Komar, A.A., and Adzhubei, I.A., Nonuniform Size Distribution of Nascent Globin Peptides, Evidence for Pause Localization Sites, and a Cotranslational Protein-Folding Model, J. Prot. Chem., 1991, vol. 10, pp. 445-453.

    Google Scholar 

  26. Makhoul, C. and Trifonov, E.N., Periodical Recurrence of Translation Pause Sites in mRNA and Standard Sizes of Protein Sequence Segments and Independently Folding Domains, J. Biomol. Struct. Dyn., 1997, vol. 14, pp. 787-788.

    Google Scholar 

  27. Trifonov, E.N., Denisov, D.A., and Makhoul, C., Interacting Sequence Patterns, Math. Model. Sci. Comput., 1998, vol. 9, pp. 24-29.

    Google Scholar 

  28. Beckmann, J.S. and Trifonov, E.N., Splice Junctions Follow a 205-base Ladder, Proc. Natl. Acad. Sci. USA, 1991, vol. 88, pp. 2380-2383.

    Google Scholar 

  29. Denisov, D.A., Shpigelman, E.S., and Trifonov, E.N., Protective Nucleosome Centering at Splice Sites as Suggested by Sequence-Directed Mapping of the Nucleosomes, Gene, 1997, vol. 205, pp. 145-149.

    Google Scholar 

  30. Trifonov, E.N., Elucidating Sequence Codes: Three Codes for Evolution, Ann. N.Y. Acad. Sci., 1999, vol. 870, pp. 330-338.

    Google Scholar 

  31. Trifonov, E.N., On the Recombinational Origin of Protein-Sequence-Subunit Structure, J. Mol. Evol., 1994, vol. 38, pp. 543-546.

    Google Scholar 

  32. Trifonov, E.N., Hidden Segmentation of Protein Sequences: Structural Connection with DNA, in Modelling of Biomolecular Structures and Mechanisms, Pullman, A., Jortner, J., and Pullman, B., Eds., Dordrecht: Kluwer Academic, 1995, pp. 473-479.

    Google Scholar 

  33. Reanney, D., Bacteriol. Rev., 1976, vol. 40, pp. 552-590.

    Google Scholar 

  34. Doolittle, R.F., The Multiplicity of Domains in Proteins, Ann. Rev. Biochem., 1995, vol. 64, pp. 287-314.

    Google Scholar 

  35. Jacobson, R.H., Zhang, X.-J., DuBose, R.F., and Matthews, B.W., Three-dimensional Structure of Beta-galactosidase from E. coli, Nature, 1994, vol. 369, pp. 761-766.

    Google Scholar 

  36. Politou, A., Gautel, M., Importa, S., et al., The Elastic I-band Region of Titin Is Assembled in a "Modular" Fashion by Weakly Interacting Ig-like Domains, J. Mol. Biol., 1996, vol. 255, pp. 604-616.

    Google Scholar 

  37. McNamara, P.T., Bolshoy, A., Trifonov, E.N., and Harrington, R.E., Sequence-Dependent Kinks Induced in Curved DNA, J. Biomol. Struct. Dyn., 1990, vol. 8, pp. 529-538.

    Google Scholar 

  38. Jurka, J., Klonowski, P., and Trifonov, E.N., Mammalian Retroposons Integrate at Sequence-Dependent DNA Kinks, J. Biomol. Struct. Dyn., 1998, vol. 15, pp. 717-721.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel

    E. N. Trifonov

  2. Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa, 31905, 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. Segmented Genome: Elementary Units of Genome Structure. Russian Journal of Genetics 38, 659–663 (2002). https://doi.org/10.1023/A:1016091917759

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1016091917759

Keywords

Search

Navigation