title: Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum.
abstract: BACKGROUND
  The ability of the human malarial parasite Plasmodium falciparum to invade, colonise and multiply within diverse host environments, as well as to manifest its virulence within the human host, are activities tightly linked to the temporal and spatial control of gene expression. Yet, despite the wealth of high throughput transcriptomic data available for this organism there is very little information regarding the location of key transcriptional landmarks or their associated cis-acting regulatory elements. Here we provide a systematic exploration of the size and organisation of transcripts within intergenic regions to yield surrogate information regarding transcriptional landmarks, and to also explore the spatial and temporal organisation of transcripts over these poorly characterised genomic regions.
  
  
  RESULTS
  Utilising the transcript data for a cohort of 105 genes we demonstrate that the untranscribed regions of mRNA are large and apportioned predominantly to the 5' end of the open reading frame. Given the relatively compact size of the P. falciparum genome, we suggest that whilst transcriptional units are likely to spatially overlap, temporal co-transcription of adjacent transcriptional units is actually limited. Critically, the size of intergenic regions is directly dependent on the orientation of the two transcriptional units arrayed over them, an observation we extend to an analysis of the complete sequences of twelve additional organisms that share moderately compact genomes.
  
  
  CONCLUSIONS
  Our study provides a theoretical framework that extends our current understanding of the transcriptional landscape across the P. falciparum genome. Demonstration of a consensus gene-spacing rule that is shared between P. falciparum and ten other moderately compact genomes of apicomplexan parasites reveals the potential for our findings to have a wider impact across a phylum that contains many organisms important to human and veterinary health.
authors.affiliation: Institute for Science and Technology in Medicine, Keele University, Huxley Building, Staffordshire ST5 5BG, United Kingdom.
authors.forename: Karen
authors.initials: K
authors.lastname: Russell
authors.forename: Sandra
authors.initials: S
authors.lastname: Hasenkamp
authors.forename: Richard
authors.initials: R
authors.lastname: Emes
authors.forename: Paul
authors.initials: P
authors.lastname: Horrocks
mesh_terms: D000818:Animals; D021901:DNA, Intergenic / Q000235:genetics*; D004912:Erythrocytes / Q000469:parasitology; D006801:Humans; D008288:Malaria / Q000469:parasitology*; D010963:Plasmodium falciparum / Q000235:genetics* / Q000502:physiology; D062211:Spatio-Temporal Analysis; D014158:Transcription, Genetic / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D020506:Untranslated Regions