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Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites
BACKGROUND: Homopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum rep...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194402/ https://www.ncbi.nlm.nih.gov/pubmed/25281558 http://dx.doi.org/10.1186/1471-2164-15-848 |
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author | Russell, Karen Cheng, Chia-Ho Bizzaro, Jeffrey W Ponts, Nadia Emes, Richard D Le Roch, Karine Marx, Kenneth A Horrocks, Paul |
author_facet | Russell, Karen Cheng, Chia-Ho Bizzaro, Jeffrey W Ponts, Nadia Emes, Richard D Le Roch, Karine Marx, Kenneth A Horrocks, Paul |
author_sort | Russell, Karen |
collection | PubMed |
description | BACKGROUND: Homopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions. RESULTS: We describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences. CONCLUSIONS: Previous comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-848) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4194402 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41944022014-10-14 Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites Russell, Karen Cheng, Chia-Ho Bizzaro, Jeffrey W Ponts, Nadia Emes, Richard D Le Roch, Karine Marx, Kenneth A Horrocks, Paul BMC Genomics Research Article BACKGROUND: Homopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions. RESULTS: We describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences. CONCLUSIONS: Previous comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-848) contains supplementary material, which is available to authorized users. BioMed Central 2014-10-03 /pmc/articles/PMC4194402/ /pubmed/25281558 http://dx.doi.org/10.1186/1471-2164-15-848 Text en © Russell et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Russell, Karen Cheng, Chia-Ho Bizzaro, Jeffrey W Ponts, Nadia Emes, Richard D Le Roch, Karine Marx, Kenneth A Horrocks, Paul Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title | Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title_full | Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title_fullStr | Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title_full_unstemmed | Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title_short | Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites |
title_sort | homopolymer tract organization in the human malarial parasite plasmodium falciparum and related apicomplexan parasites |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194402/ https://www.ncbi.nlm.nih.gov/pubmed/25281558 http://dx.doi.org/10.1186/1471-2164-15-848 |
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