Characteristic Enrichment of DNA Repeats in Different Genomes

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 tha...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 1997-05, Vol.94 (10), p.5237-5242
Main Authors: Cox, Randal, Mirkin, Sergei M.
Format: Article
Language:English
Subjects:
Algorithms
Animals
Bacteria
Base Composition
Base Sequence
Biological Sciences
Caenorhabditis elegans - genetics
Cyanobacteria - genetics
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
Escherichia coli - genetics
Eukaryotic cells
Genetic Code
Genetic Markers
Genetics
Genome
Genome, Bacterial
Genomes
Genomics
Haemophilus influenzae - genetics
Humans
Methanococcus - genetics
Nucleic Acid Conformation
Nucleic acids
Organelles
Palindromes
Probability
Purines
Pyrimidines
Ratios
Repetitive Sequences, Nucleic Acid
Saccharomyces cerevisiae - genetics
Species Specificity
Tandem repeat sequences
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.94.10.5237