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Background  There are very few molecular genetic tools available to study the apicomplexan parasite  Cryptosporidium parvum . The organism is not amenable to continuous  in vitro  cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in  C. parvum .    Results  We have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of  in vitro  epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinant  C. parvum  DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters.    Conclusion  Several DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential  cis -regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a global  C. parvum  gene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile