Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites

BMC Genomics

Paul Horrocks⁷  Kenneth A Marx²  Karine Le Roch⁶  Richard D Emes¹  Nadia Ponts⁴  Jeffrey W Bizzaro³  Chia-Ho Cheng⁵  Karen Russell⁷ 

[1]Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK

[2]Center for Intelligent Biomaterials, University of Massachusetts Lowell, Lowell, MA 01854, USA

[3]Bioinformatics Organization Inc, Hudson, MA 01749, USA

[4]National Institute for Agricultural Research (INRA), UR1264-Mycology and Food Safety (MycSA), CS20032, 33882 Villenave d’Ornon Cedex, France

[5]Currently at Institute for Aging Research, Hebrew SeniorLife, Boston, MA 02131, USA

[6]Department Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA

[7]Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent ST5 5BG, Staffordshire, UK

关键词: Gene expression;    Nucleosome;    Malaria;    Intergenic regions;    Poly dA.dT;   

Others  :  1139155
DOI  :  10.1186/1471-2164-15-848

 received in 2014-05-21, accepted in 2014-09-24,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Russell et al.; licensee BioMed Central Ltd.

【 图 表 】

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