Scaling features of noncoding DNA

H. E. Stanley; S. V. Buldyrev; A. L. Goldberger; S. Havlin; C. K. Peng; M. Simons

doi:10.1016/S0378-4371(99)00407-0

Scaling features of noncoding DNA

H. E. Stanley, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C. K. Peng, M. Simons

Department of Physics

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

104 Scopus citations

Abstract

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range - indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

Original language	English
Pages (from-to)	1-18
Number of pages	18
Journal	Physica A: Statistical Mechanics and its Applications
Volume	273
Issue number	1-2
DOIs	https://doi.org/10.1016/S0378-4371(99)00407-0
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 are grateful to many individuals, including R.N. Mantegna, M.E. Matsa, S.M. Ossadnik, and F. Sciortino, for major contributions to those results reviewed here that represent collaborative research efforts. We also wish to thank C. Cantor, C. DeLisi, M. Frank-Kamenetskii, A.Yu. Grosberg, G. Huber, I. Labat, L. Liebovitch, G.S. Michaels, P. Munson, R. Nossal, R. Nussinov, R.D. Rosenberg, J.J. Schwartz, M. Schwartz, E.I. Shakhnovich, M.F. Shlesinger, N. Shworak, and E.N. Trifonov for valuable discussions. Partial support was provided by the National Science Foundation, National Institutes of Health (Center for Biomedical Signals and Human Genome Project), the G. Harold and Leila Y. Mathers Charitable Foundation, the National Heart, Lung and Blood Institute, the National Aeronautics and Space Administration, the Israel-USA Binational Science Foundation, Israel Academy of Sciences, and (to C-KP) by an NIH/NIMH Postdoctoral NRSA Fellowship.

Funding

We are grateful to many individuals, including R.N. Mantegna, M.E. Matsa, S.M. Ossadnik, and F. Sciortino, for major contributions to those results reviewed here that represent collaborative research efforts. We also wish to thank C. Cantor, C. DeLisi, M. Frank-Kamenetskii, A.Yu. Grosberg, G. Huber, I. Labat, L. Liebovitch, G.S. Michaels, P. Munson, R. Nossal, R. Nussinov, R.D. Rosenberg, J.J. Schwartz, M. Schwartz, E.I. Shakhnovich, M.F. Shlesinger, N. Shworak, and E.N. Trifonov for valuable discussions. Partial support was provided by the National Science Foundation, National Institutes of Health (Center for Biomedical Signals and Human Genome Project), the G. Harold and Leila Y. Mathers Charitable Foundation, the National Heart, Lung and Blood Institute, the National Aeronautics and Space Administration, the Israel-USA Binational Science Foundation, Israel Academy of Sciences, and (to C-KP) by an NIH/NIMH Postdoctoral NRSA Fellowship.

Funders	Funder number
Israel-USA Binational Science Foundation
NIH/NIMH
National Science Foundation
National Institutes of Health
National Aeronautics and Space Administration
G. Harold and Leila Y. Mathers Charitable Foundation
Israel National Road Safety Authority
Israel Academy of Sciences and Humanities

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10.1016/S0378-4371(99)00407-0

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title = "Scaling features of noncoding DNA",

abstract = "We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range - indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the {"}redundancy{"} of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong {"}background{"} effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.",

author = "Stanley, {H. E.} and Buldyrev, {S. V.} and Goldberger, {A. L.} and S. Havlin and Peng, {C. K.} and M. Simons",

note = "Funding Information: We are grateful to many individuals, including R.N. Mantegna, M.E. Matsa, S.M. Ossadnik, and F. Sciortino, for major contributions to those results reviewed here that represent collaborative research efforts. We also wish to thank C. Cantor, C. DeLisi, M. Frank-Kamenetskii, A.Yu. Grosberg, G. Huber, I. Labat, L. Liebovitch, G.S. Michaels, P. Munson, R. Nossal, R. Nussinov, R.D. Rosenberg, J.J. Schwartz, M. Schwartz, E.I. Shakhnovich, M.F. Shlesinger, N. Shworak, and E.N. Trifonov for valuable discussions. Partial support was provided by the National Science Foundation, National Institutes of Health (Center for Biomedical Signals and Human Genome Project), the G. Harold and Leila Y. Mathers Charitable Foundation, the National Heart, Lung and Blood Institute, the National Aeronautics and Space Administration, the Israel-USA Binational Science Foundation, Israel Academy of Sciences, and (to C-KP) by an NIH/NIMH Postdoctoral NRSA Fellowship. ; Proceedings of the 1999 13th Max Born Symposium on 'Statistical Physics in Biology: Perspectives in DNA Analysis, Population Dynamics and Ageing' ; Conference date: 26-05-1999 Through 30-05-1999",

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AU - Simons, M.

N1 - Funding Information: We are grateful to many individuals, including R.N. Mantegna, M.E. Matsa, S.M. Ossadnik, and F. Sciortino, for major contributions to those results reviewed here that represent collaborative research efforts. We also wish to thank C. Cantor, C. DeLisi, M. Frank-Kamenetskii, A.Yu. Grosberg, G. Huber, I. Labat, L. Liebovitch, G.S. Michaels, P. Munson, R. Nossal, R. Nussinov, R.D. Rosenberg, J.J. Schwartz, M. Schwartz, E.I. Shakhnovich, M.F. Shlesinger, N. Shworak, and E.N. Trifonov for valuable discussions. Partial support was provided by the National Science Foundation, National Institutes of Health (Center for Biomedical Signals and Human Genome Project), the G. Harold and Leila Y. Mathers Charitable Foundation, the National Heart, Lung and Blood Institute, the National Aeronautics and Space Administration, the Israel-USA Binational Science Foundation, Israel Academy of Sciences, and (to C-KP) by an NIH/NIMH Postdoctoral NRSA Fellowship.

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N2 - We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range - indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

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Scaling features of noncoding DNA

Abstract

Bibliographical note

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