title: In silico discovery of transcription regulatory elements in Plasmodium falciparum.
abstract: BACKGROUND
  With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying networks of transcriptional control important for the progression of the parasite life cycle is highly pertinent to the development of new anti-malarials. To date, relatively little is known regarding the specific mechanisms the parasite employs to regulate gene expression at the mRNA level, with studies of the P. falciparum genome sequence having revealed few cis-regulatory elements and associated transcription factors. Although it is possible the parasite may evoke mechanisms of transcriptional control drastically different from those used by other eukaryotic organisms, the extreme AT-rich nature of P. falciparum intergenic regions (approximately 90% AT) presents significant challenges to in silico cis-regulatory element discovery.
  
  
  RESULTS
  We have developed an algorithm called Gene Enrichment Motif Searching (GEMS) that uses a hypergeometric-based scoring function and a position-weight matrix optimization routine to identify with high-confidence regulatory elements in the nucleotide-biased and repeat sequence-rich P. falciparum genome. When applied to promoter regions of genes contained within 21 co-expression gene clusters generated from P. falciparum life cycle microarray data using the semi-supervised clustering algorithm Ontology-based Pattern Identification, GEMS identified 34 putative cis-regulatory elements associated with a variety of parasite processes including sexual development, cell invasion, antigenic variation and protein biosynthesis. Among these candidates were novel motifs, as well as many of the elements for which biological experimental evidence already exists in the Plasmodium literature. To provide evidence for the biological relevance of a cell invasion-related element predicted by GEMS, reporter gene and electrophoretic mobility shift assays were conducted.
  
  
  CONCLUSIONS
  This GEMS analysis demonstrates that in silico regulatory element discovery can be successfully applied to challenging repeat-sequence-rich, base-biased genomes such as that of P. falciparum. The fact that regulatory elements were predicted from a diverse range of functional gene clusters supports the hypothesis that cis-regulatory elements play a role in the transcriptional control of many P. falciparum biological processes. The putative regulatory elements described represent promising candidates for future biological investigation into the underlying transcriptional control mechanisms of gene regulation in malaria parasites.
authors.affiliation: Department of Cell Biology, ICND 202, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jayoung@scripps.edu
authors.forename: Jason A
authors.initials: JA
authors.lastname: Young
authors.forename: Jeffery R
authors.initials: JR
authors.lastname: Johnson
authors.forename: Chris
authors.initials: C
authors.lastname: Benner
authors.forename: S Frank
authors.initials: SF
authors.lastname: Yan
authors.forename: Kaisheng
authors.initials: K
authors.lastname: Chen
authors.forename: Karine G
authors.initials: KG
authors.lastname: Le Roch
authors.forename: Yingyao
authors.initials: Y
authors.lastname: Zhou
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Winzeler
mesh_terms: D000465:Algorithms; D000818:Animals; D000940:Antigenic Variation / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004261:DNA Replication; D004912:Erythrocytes / Q000378:metabolism / Q000469:parasitology; D018503:Genome, Protozoan / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics; D008957:Models, Genetic; D005810:Multigene Family; D010963:Plasmodium falciparum / Q000235:genetics* / Q000254:growth & development / Q000276:immunology / Q000472:pathogenicity; D014176:Protein Biosynthesis / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D046468:Sexual Development / Q000235:genetics; D034101:Sporozoites / Q000378:metabolism