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

BMC Genomics

Research Article

Sandeep J Joseph¹  Jenna Oberstaller²  Jessica C Kissinger³ 

[1] Center for Tropical and Emerging Global Diseases, University of Georgia, 30602, Athens, GA, USA;Center for Tropical and Emerging Global Diseases, University of Georgia, 30602, Athens, GA, USA;Department of Genetics, University of Georgia, 30602, Athens, GA, USA;Center for Tropical and Emerging Global Diseases, University of Georgia, 30602, Athens, GA, USA;Department of Genetics, University of Georgia, 30602, Athens, GA, USA;Institute of Bioinformatics, University of Georgia, 30602, Athens, GA, USA;

关键词: Apicomplexa;    Transcription;    Gene regulation;    Motif;    AP2;    E2F;    G-box;   

DOI  :  10.1186/1471-2164-14-516

 received in 2013-03-12, accepted in 2013-07-09,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThere 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.ResultsWe 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.ConclusionSeveral 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.

【 授权许可】

Unknown   
© Oberstaller et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.