title: Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.
abstract: 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.
authors.forename: Karen
authors.initials: K
authors.lastname: Russell
authors.forename: Chia-Ho
authors.initials: CH
authors.lastname: Cheng
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Bizzaro
authors.forename: Nadia
authors.initials: N
authors.lastname: Ponts
authors.forename: Richard D
authors.initials: RD
authors.lastname: Emes
authors.forename: Karine
authors.initials: K
authors.lastname: Le Roch
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Marx
authors.affiliation: Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent ST5 5BG, Staffordshire, UK. p.d.horrocks@keele.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Horrocks
mesh_terms: D021901:DNA, Intergenic / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D018503:Genome, Protozoan; D006801:Humans; D008288:Malaria / Q000469:parasitology* / Q000473:pathology; D009707:Nucleosomes / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D010963:Plasmodium falciparum / Q000235:genetics* / Q000378:metabolism; D011067:Poly dA-dT / Q000737:chemistry / Q000378:metabolism; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D009707:Nucleosomes; D020506:Untranslated Regions; D011067:Poly dA-dT