DOI: 10.1073/pnas.94.10.5237. Characteristic enrichment of DNA repeats in different genomes

Characteristic enrichment of DNA repeats in different genomes

10.1073/pnas.94.10.5237

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Using computer programs developed for this purpose, we searched for various repeated sequences including inverted, direct tandem, and homopurine–homopyrimidine mirror repeats in various prokaryotes, eukaryotes, and an archaebacterium. Comparison of observed frequencies with expectations revealed that in bacterial genomes and organelles the frequency of different repeats is either random or enriched for inverted and/or direct tandem repeats. By contrast, in all eukaryotic genomes studied, we observed an overrepresentation of all repeats, especially homopurine–homopyrimidine mirror repeats. Analysis of the genomic distribution of all abundant repeats showed that they are virtually excluded from coding sequences. Unexpectedly, the frequencies of abundant repeats normalized for their expectations were almost perfect exponential functions of their size, and for a given repeat this function was indistinguishable between different genomes.

Bibliography

Cox, R., & Mirkin, S. M. (1997). Characteristic enrichment of DNA repeats in differentâgenomes. Proceedings of the National Academy of Sciences, 94(10), 5237â5242.

Authors 2

Randal Cox (first)
Sergei M. Mirkin (additional)

References 39 Referenced 99

10.1016/0022-2836(85)90262-1
10.1016/S0168-9525(00)89076-9
10.1080/07391102.1989.10506528
10.1080/07391102.1989.10506529
10.1038/ng0296-183
10.1128/jb.174.14.4583-4593.1992
R R Sinden DNA Structure and Function (Academic, San Diego, 1994). / DNA Structure and Function by Sinden R R (1994)
10.1073/pnas.77.11.6468
10.1146/annurev.bb.23.060194.002545
10.1146/annurev.bi.53.070184.004043
10.1093/nar/13.12.4343
10.1080/07391102.1985.10508420
10.1073/pnas.93.16.8524
10.1073/pnas.93.12.5854
10.1093/nar/21.16.3875
10.1126/science.8430316
10.1093/nar/23.11.1977
10.1016/S0021-9258(19)49776-7
10.1016/0014-5793(85)80769-9
10.1007/BF00352220
10.1021/bi9601013
10.1093/nar/24.11.1992
10.1073/pnas.93.4.1560
10.1074/jbc.270.48.28970
10.1016/0959-4388(93)90149-S
10.1038/330495a0
10.1021/bi00398a050
10.1093/nar/16.4.1517
10.1007/BF02138367
10.1080/07391102.1991.10507919
10.1086/407817
10.1016/0022-2836(81)90264-3
R E Walpole, R H Myers Probability and Statistics for Engineers and Scientists (Macmillan, New York, 1985). / Probability and Statistics for Engineers and Scientists by Walpole R E (1985)
10.1146/annurev.mi.48.100194.003155
A Vologodskii Topology and Physics of Circular DNA (CRC, Boca Raton, FL, 1992). / Topology and Physics of Circular DNA by Vologodskii A (1992)
R D Wells, R R Sinden Genome Analysis, eds K E Davies, S T Warren (Cold Spring Harbor Lab. Press, Plainview, NY) 7, 107–138 (1993). / Genome Analysis by Wells R D (1993)
10.1126/science.273.5278.1058
J Morris, S R Kushner, R Ivarie Mol Biol Evol 3, 343–355 (1986). / Mol Biol Evol by Morris J (1986)
10.1093/nar/22.9.1735

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:31 a.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 2:50 p.m.)
Indexed	3 weeks, 5 days ago (Aug. 5, 2025, 8:13 a.m.)
Issued	28 years, 3 months ago (May 13, 1997)
Published	28 years, 3 months ago (May 13, 1997)
Published Online	28 years, 3 months ago (May 13, 1997)
Published Print	28 years, 3 months ago (May 13, 1997)

Funders 0

None

BibTeX

@article{Cox_1997, title={Characteristic enrichment of DNA repeats in different genomes}, volume={94}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.94.10.5237}, DOI={10.1073/pnas.94.10.5237}, number={10}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Cox, Randal and Mirkin, Sergei M.}, year={1997}, month=may, pages={5237–5242} }

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