Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis

Gene

Volumn 300, Issue 1-2, 2002, Pages 203-211

  Fukushima, Atsushi ^a   Ikemura, Toshimichi ^b,c   Kinouchi, Makoto ^c,d   Oshima, Taku ^a,c   Kudo, Yoshihiro ^c,d   Mori, Hirotada ^a   Kanaya, Shigehiko ^a,d  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d YAMAGATA UNIVERSITY   (Japan)

Author keywords

Fourier analysis; Long range correlation; Nucleotide periodicity; Power spectrum analysis; Tandem repeat

Indexed keywords

DNA; NUCLEOTIDE;

ANALYTIC METHOD; ARCHAEBACTERIUM; CAENORHABDITIS ELEGANS; CHROMOSOME 21; CHROMOSOME 22; CHROMOSOME ANALYSIS; CONFERENCE PAPER; DNA STRUCTURE; EUKARYOTE; GENETIC ANALYSIS; GENOME; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PERIODICITY; POWER SPECTRUM; PREVALENCE; PRIORITY JOURNAL; PROKARYOTE; SEQUENCE ANALYSIS; THERMOPHILIC BACTERIUM; WORM;

ANIMALS; ARCHAEA; BACTERIA; BASE COMPOSITION; CAENORHABDITIS ELEGANS; CHROMOSOMES; CHROMOSOMES, HUMAN, PAIR 21; CHROMOSOMES, HUMAN, PAIR 22; DNA; EUKARYOTIC CELLS; GENOME; HUMANS; PROKARYOTIC CELLS; SEQUENCE ANALYSIS, DNA;

ARCHAEA; BACTERIA (MICROORGANISMS); CAENORHABDITIS; CAENORHABDITIS ELEGANS; EUKARYOTA; PROKARYOTA;

EID: 0037202373     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(02)00850-8     Document Type: Conference Paper

References (53)

1. Arneodo A., Bacry E., Graves P.V., Muzy J.F. Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett. 74:1995;3293-3296.
2. Arneodo A., d'Aubenton-Carafa Y., Bacry E., Graves P.V., Muzy J.F., Thermes C. Wavelet based fractal analysis of DNA sequences. Physica D. 96:1996;291-320.
3. Audit B., Thermes C., Vaillant C., d'Aubenton-Carafa Y., Muzy J.F., Arneodo A. Long-range correlations in genomic DNA: a signature of the nucleosomal structure. Phys. Rev. Lett. 86:2001;2471-2474.
4. Bernardi G. The isochore organization of the human genome. Annu. Rev. Genet. 23:1989;637-661.
5. Bernardi G. Isochores and the evolutionary genomics of vertebrates: organization of the human genome. Gene. 241:2000;3-17.
6. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 228:1985;953-958.
7. Bolshoy A., McNamara P., Harrington R.E., Trifonov E.N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA. 88:1991;2312-2316.
8. Buldyrev S.V., Goldberger A.L., Havlin S., Mantegna R.N., Matsa M.E., Peng C.-K., Simons M., Stanley H.E. Long-range correlation properties od coding and non-coding DNA sequences: GenBank analysis. Phys. Rev. E. 51:1995;5084-5091.
9. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282:1998;2012-2018.
10. 2+. Biophys. J. 73:1997;348-356.
11. Comings D.E., Okada T.A. Holocentric chromosomes in Oncopeltus: kinetochore plates are present in mitosis but absent in meiosis. Chromosoma. 37:(2):1972;177-192.
12. Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., et al. The DNA sequence of human chromosome 22. Nature. 402:1999;489-495.
13. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10:1982;5303-5318.
14. Grosse I., Herzel H., Buldyrev S.V., Stanley H.E. Species independence of mutual information in coding and non-coding DNA. Phys. Rev. E. 61:2000;5624-5629.
15. Gutierrez G., Oliver J.L., Marin A. On the origin of the periodicity of three in protein coding DNA sequences. J. Theor. Biol. 167:1994;413-414.
16. Hattori M., Fujiyama A., Taylor T.D. The DNA sequence of human chromosome 21. Nature. 405:2000;311-319.
17. Herzel H. Entropies of biosequences: the role of repeats. Phys. Rev. E. 50:1994;5061-5071.
18. Herzel H. Correlations in DNA sequences: the role of coding segments. Phys. Rev. E. 55:1997;800-810.
19. Herzel H., Weiss O., Trifonov E.N. 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics (CABIOS). 15:1999;187-193.
20. Holmquist G.P. Evolution of chromosome bands: molecular ecology of non-coding DNA. J. Mol. Evol. 28:1989;469-486.
21. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
22. Ikemura T., Aota S. Global variation in G+C content along vertebrate genome DNA: possible correlation with chromosome band structures. J. Mol. Biol. 203:1988;1-13.
23. Karlin S., Brendel V. Patchiness and correlations in DNA sequences. Science. 259:1993;677-680.
24. Katti M.V., Ranjeker P.K., Gupta V.S. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 18:2001;1161-1167.
25. Kirillova O.V. Comparative statistical analysis of bacteria genomes in 'word' context. Physica A. 290:2001;453-463.
26. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
27. Li W. Expansion-modification systems: a model for spatial 1/f spectra. Phys. Rev. A. 43:1991;5240-5260.
28. Li W. Generating non-trivial long-range correlations and 1/f spectra by replication and mutation. Int. J. Bifurcation Chaos. 2:1992;137-154.
29. α spectrum in a non-coding DNA sequence. Europhys. Lett. 17:1992;655-660.
30. Li W., Stolovitzky G., Bernaola-Galvan P., Oliver J.L. Compositonal heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes. Gen. Res. 8:1998;916-918.
31. Lu X., Sun Z., Chen H., Li Y. Characterizing self-similarity in bacteria DNA sequences. Phys. Rev. E. 58:1998;3578-3584.
32. Mantegna R.N., Buldyrev S.V., Goldberger A.L., Havlin S., Peng C.-K., Simons M., Stanley H.E. Linguistic features of non-coding DNA sequences. Phys. Rev. Lett. 73:1994;3169-3172.
33. Oliver J., Bernaola-Galván P., Carpena P., Román-Roldán R. Isochore chromosome map of eukaryotic genomes. Gene. 276:2001;47-56.
34. Pavliček A., Jabbari K., Pacčes J., Pacčes V., Hejnar J., Bernardi G. Similar integration but different stability of Alus and LINEs in the human genome. Gene. 276:2001;39-45.
35. Peng C.-K., Buldyrev S.V., Goldberger A.L., Havlin S., Sciortino F., Simons M., Stanley H.E. Long-range correlations in nucleotide sequences. Nature. 356:1992;168-170.
36. Peng C.-K., Buldyrev S.V., Havlin S., Simons M., Stanley H.E., Goldberger A.L. Mosaic organization of DNA nucleotides. Phys. Rev. E. 49:1994;1685-1689.
37. Sandman K., Reeve J.N. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch. Microbiol. 173:2000;165-169.
38. Sanford C., Perry M.D. Asymmetrically distributed oligonucleotide repeats in the Caenorhabditis elegans genome sequence that map to regions important for meiotic chromosome segregation. Nucleic Acids Res. 29:2001;2920-2926.
39. Shepherd J.C. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17:1981;94-102.
40. Shepherd J.C.W. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl. Acad. Sci. USA. 78:1981;1596-1600.
41. Sinden R.R. DNA Structure and Function. 1994;Academic Press, Inc, San Diego.
42. Staden R. Finding protein coding regions in genomic sequences. Methods Enzymol. 183:1990;163-180.
43. Tomita M., Wada M., Kawashima Y. ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes. J. Mol. Evol. 49:1999;182-192.
44. Trifonov E.N. 3-, 10.5-, 200- and 400-base periodicities in genome sequences. Physica A. 249:1998;511-516.
45. Trifonov E.V., Sussman J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA. 77:1980;3816-3820.
46. Tsonis A.A., Elsner J.B., Tsonis P.A. Periodicity in DNA coding sequences: implications in gene evolution. J. Theor. Biol. 151:1991;323-331.
47. Usdin K. NGG-triplet repeats form similar intrastrand structures: implications for the triplet expansion diseases. Nucleic Acids Res. 26:1998;4078-4085.
48. Venter J.C., Adams M.D., Myers E.W. The sequence of the human genome. Science. 291:2001;1304-1351.
49. Vieira M. Statistics of DNA sequences: a low-frequency analysis. Phys. Rev. E. 60:1999;5932-5937.
50. Vologodsky A. Topology and Physics of Circular DNA. 1992;CRC Press, Boca Raton.
51. Voss R.F. Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys. Rev. Lett. 68:1992;3805-3808.
52. Watanabe Y., Fujiyama A., Ichiba Y., Hattori M., Yada T., Sakaki Y., Ikemura T. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum. Mol. Genet. 11:2002;3-21.
53. Yu Z.G., Anh V.V., Wang B. Correlation property of length sequences based on global structure of the complete genome. Phys. Rev. Lett. E. 63:2001;0119031-0119038.