Length distributions of simple tandem repeats in genomes

Su-Long Nyeo, Jui Ping Yu

Research output: Contribution to journalArticle

Abstract

The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.

Original languageEnglish
Pages (from-to)299-312
Number of pages14
JournalJournal of Biological Systems
Volume15
Issue number3
DOIs
Publication statusPublished - 2007 Sep 1

Fingerprint

Tandem Repeat Sequences
tandem repeat sequences
Genome
Pan troglodytes
genome
Genes
Cytosine
Methylation
Unit
Tail
cytosine
DNA sequences
Chromosomes
Nucleotides
Interspersed Repetitive Sequences
Dinucleotide Repeats
Rats
Deamination
Thymine
tail

All Science Journal Classification (ASJC) codes

  • Agricultural and Biological Sciences (miscellaneous)
  • Ecology
  • Applied Mathematics

Cite this

@article{c16dd64e777846f4ab42384afdf53952,
title = "Length distributions of simple tandem repeats in genomes",
abstract = "The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.",
author = "Su-Long Nyeo and Yu, {Jui Ping}",
year = "2007",
month = "9",
day = "1",
doi = "10.1142/S0218339007002246",
language = "English",
volume = "15",
pages = "299--312",
journal = "Journal of Biological Systems",
issn = "0218-3390",
publisher = "World Scientific Publishing Co. Pte Ltd",
number = "3",

}

Length distributions of simple tandem repeats in genomes. / Nyeo, Su-Long; Yu, Jui Ping.

In: Journal of Biological Systems, Vol. 15, No. 3, 01.09.2007, p. 299-312.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Length distributions of simple tandem repeats in genomes

AU - Nyeo, Su-Long

AU - Yu, Jui Ping

PY - 2007/9/1

Y1 - 2007/9/1

N2 - The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.

AB - The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.

UR - http://www.scopus.com/inward/record.url?scp=34748845667&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34748845667&partnerID=8YFLogxK

U2 - 10.1142/S0218339007002246

DO - 10.1142/S0218339007002246

M3 - Article

VL - 15

SP - 299

EP - 312

JO - Journal of Biological Systems

JF - Journal of Biological Systems

SN - 0218-3390

IS - 3

ER -