Distinct frequency-distributions of homopolymeric DNA tracts in different genomes - PubMed (original) (raw)
Comparative Study
Distinct frequency-distributions of homopolymeric DNA tracts in different genomes
K J Dechering et al. Nucleic Acids Res. 1998.
Abstract
The unusual base composition of the genome of the human malaria parasite Plasmodium falciparum prompted us to systematically investigate the occurrence of homopolymeric DNA tracts in the P. falciparum genome and, for comparison, in the genomes of Homo sapiens , Saccharomyces cerevisiae , Caenorhabditis elegans , Arabidopsis thaliana , Escherichia coli and Mycobacterium tuberculosis. Comparison of theobserved frequencies with the frequencies as expected for random DNA revealed that homopolymeric (dA:dT) tracts occur well above chance in the eukaryotic genome. In the majority of these genomes, (dA:dT) tract overrepresentation proved to be an exponential function of the tract length. (dG:dC) tract overrepresentation was absent or less pronounced in both prokaryotic and eukaryotic genomes. On the basis of our results, we propose that homopolymeric (dA:dT) tracts are expanded via replication slippage. This slippage-mediated expansion does not operate on tracts with lengths below a critical threshold of 7-10 bp.
Similar articles
- Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.
Russell K, Cheng CH, Bizzaro JW, Ponts N, Emes RD, Le Roch K, Marx KA, Horrocks P. Russell K, et al. BMC Genomics. 2014 Oct 3;15(1):848. doi: 10.1186/1471-2164-15-848. BMC Genomics. 2014. PMID: 25281558 Free PMC article. - Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition.
Zhou Y, Bizzaro JW, Marx KA. Zhou Y, et al. BMC Genomics. 2004 Dec 14;5:95. doi: 10.1186/1471-2164-5-95. BMC Genomics. 2004. PMID: 15598342 Free PMC article. - OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS. Li L, et al. Genome Res. 2003 Sep;13(9):2178-89. doi: 10.1101/gr.1224503. Genome Res. 2003. PMID: 12952885 Free PMC article. - [Structural-functional organization of the poly[(dG-dT).(dC-dA)] sequence in the genome of eukaryotic organisms].
Vashakidze RP, Mamulashvili NA, Gabriadze IIu. Vashakidze RP, et al. Mol Biol (Mosk). 1990 Jan-Feb;24(1):10-6. Mol Biol (Mosk). 1990. PMID: 2190079 Review. Russian. No abstract available. - Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome.
Florent I, Maréchal E, Gascuel O, Bréhélin L. Florent I, et al. Parasite. 2010 Dec;17(4):273-83. doi: 10.1051/parasite/2010174273. Parasite. 2010. PMID: 21275233 Review.
Cited by
- Sequencing accuracy and systematic errors of nanopore direct RNA sequencing.
Liu-Wei W, van der Toorn W, Bohn P, Hölzer M, Smyth RP, von Kleist M. Liu-Wei W, et al. BMC Genomics. 2024 May 28;25(1):528. doi: 10.1186/s12864-024-10440-w. BMC Genomics. 2024. PMID: 38807060 Free PMC article. - Resolving unknown nucleotides in the IPD-IMGT/HLA database by extended and full-length sequencing of HLA class I and II alleles.
Voorter CEM, Groeneweg M, Olieslagers TI, Fae I, Fischer GF, Andreani M, Troiano M, Vidan-Jeras B, Montanic S, Hepkema BG, Bungener LB, Tilanus MGJ, Wieten L. Voorter CEM, et al. Immunogenetics. 2024 Apr;76(2):109-121. doi: 10.1007/s00251-024-01333-z. Epub 2024 Feb 24. Immunogenetics. 2024. PMID: 38400869 Free PMC article. - iMUT-seq: high-resolution DSB-induced mutation profiling reveals prevalent homologous-recombination dependent mutagenesis.
Bader AS, Bushell M. Bader AS, et al. Nat Commun. 2023 Dec 18;14(1):8419. doi: 10.1038/s41467-023-44167-1. Nat Commun. 2023. PMID: 38110444 Free PMC article. - Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy.
Poulet A, Kratkiewicz AJ, Li D, van Wolfswinkel JC. Poulet A, et al. Sci Adv. 2023 Oct 6;9(40):eadh4887. doi: 10.1126/sciadv.adh4887. Epub 2023 Oct 6. Sci Adv. 2023. PMID: 37801496 Free PMC article. - Comparative Genome Analysis Reveals Accumulation of Single-Nucleotide Repeats in Pathogenic Escherichia Lineages.
Ishiya K, Nakashima N. Ishiya K, et al. Curr Issues Mol Biol. 2022 Jan 20;44(2):498-504. doi: 10.3390/cimb44020034. Curr Issues Mol Biol. 2022. PMID: 35723320 Free PMC article.
References
- Nucleic Acids Res. 1992 Jan 25;20(2):211-5 - PubMed
- EMBO J. 1989 May;8(5):1517-25 - PubMed
- Nat Genet. 1994 Feb;6(2):114-6 - PubMed
- J Mol Biol. 1989 Dec 5;210(3):587-99 - PubMed
- Nature. 1986 Aug 14-20;322(6080):652-6 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases