Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

Sergey V. Buldyrev; Nikolay V. Dokholyan; Shlomo Havlin; H. Eugene Stanley; Rachel H.R. Stanley

doi:10.1016/S0378-4371(99)00338-6

Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

Sergey V. Buldyrev, Nikolay V. Dokholyan, Shlomo Havlin, H. Eugene Stanley, Rachel H.R. Stanley

Department of Physics

Research output: Contribution to journal › Conference article › peer-review

7 Scopus citations

Abstract

We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

Original language	English
Pages (from-to)	19-32
Number of pages	14
Journal	Physica A: Statistical Mechanics and its Applications
Volume	273
Issue number	1-2
DOIs	https://doi.org/10.1016/S0378-4371(99)00338-6
State	Published - 1 Nov 1999
Event	Proceedings of the 1999 13th Max Born Symposium on 'Statistical Physics in Biology: Perspectives in DNA Analysis, Population Dynamics and Ageing' - Wroclaw, Poland Duration: 26 May 1999 → 30 May 1999

Bibliographical note

Funding Information:
We would like to thank N. Broude, C. Cantor, R.S. Dokholyan, M. Frank-Kamenetskii, A. Goldberger, M. Goodman, A.Yu. Grosberg, I. Grosse, I Labat, R.N. Mantegna, C.-K. Peng, E.I. Shakhmonvich, A. Shehter, M. Simons, C. Smith, F. Starr, E.N. Trifonov, G.M. Viswanathan, G.H. Weiss, and R. Wells for fruitful discussions. This work is supported by NIH-HGP. N.V.D. is supported by NIH NRSA molecular biophysics predoctoral traineeship (GM08291-09).

Keywords

DNA
Evolution
Oligomer clustering
Percolation theory

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abstract = "We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.",

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AU - Stanley, Rachel H.R.

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N2 - We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

AB - We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

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KW - Evolution

KW - Oligomer clustering

KW - Percolation theory

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Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

Abstract

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Keywords

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