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Open Access Research

Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii

Nandita Mullapudi13*, Sandeep J Joseph1 and Jessica C Kissinger12*

Author Affiliations

1 Department of Genetics, University of Georgia, East Green Street, Athens, Georgia, 30602, USA

2 Center for Tropical and Emerging Global Diseases, University of Georgia, DW Brooks Drive, Athens, Georgia, 30602, USA

3 Current address: Department of Pulmonary Medicine, Albert Einstein College of Medicine, Morris Park Ave, Bronx, New York, NY 10461, USA

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Genome Biology 2009, 10:R34  doi:10.1186/gb-2009-10-4-r34

Published: 7 April 2009

Abstract

Background

Toxoplasma gondii is a member of the phylum Apicomplexa, which consists entirely of parasitic organisms that cause several diseases of veterinary and human importance. Fundamental mechanisms of gene regulation in this group of protistan parasites remain largely uncharacterized. Owing to their medical and veterinary importance, genome sequences are available for several apicomplexan parasites. Their genome sequences reveal an apparent paucity of known transcription factors and the absence of canonical cis-regulatory elements. We have approached the question of gene regulation from a sequence perspective by mining the genomic sequence data to identify putative cis-regulatory elements using a de novo approach.

Results

We have identified putative cis-regulatory elements present upstream of functionally related groups of genes and subsequently characterized the function of some of these conserved elements using reporter assays in the parasite. We show a sequence-specific role in gene-expression for seven out of eight identified elements.

Conclusions

This work demonstrates the power of pure sequence analysis in the absence of expression data or a priori knowledge of regulatory elements in eukaryotic organisms with compact genomes.