Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva

Kyle Tretina,Roger Pelle,Joana C Silva

doi:10.1186/s12864-016-2444-5

Abstract

BackgroundTheileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annotation now available for this parasite, offer an unprecedented opportunity to characterize the genomic features associated with gene regulation in this species. Our previous analyses revealed a T. parva genome even more gene-dense than previously thought, with many adjacent loci overlapping each other, not only at the level of untranslated sequences (UTRs) but even in coding sequences.ResultsDespite this compactness, Theileria intergenic regions show a pattern of size distribution indicative of monocistronic gene transcription. Three previously described motifs are conserved among Theileria species and highly prevalent in promoter regions near or at the transcription start sites. We found novel motifs at many transcription termination sites, as well as upstream of parasite genes thought to be critical for host transformation. Adjacent genes that could be regulated by antisense transcription from an overlapping transcriptional unit are syntenic between T. parva and P. falciparum at a frequency higher than expected by chance, suggesting the presence of common, and evolutionary old, regulatory mechanisms in the phylum Apicomplexa.ConclusionsWe propose a model of transcription with conserved sense and antisense transcription from a few taxonomically ubiquitous and several species-specific promoter motifs. Interestingly, the gene networks regulated by conserved promoters are themselves, in most cases, not conserved between species or genera.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2444-5) contains supplementary material, which is available to authorized users.

Highlights

Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle
Aside from early bioinformatics predictions of potentially functional cis regulatory motifs in the T. parva genome [11], very little is known about the basic transcriptional unit in this species
Those analyses revealed that in T. parva 5′5′ intergenic regions are significantly longer than 5′ 3′ intergenic regions, which in turn are significantly longer than 3′3′ intergenic regions, a clear signature of spatial requirements imposed by upstream regulatory motifs in a very compact genome [11,12,13]

Summary

Introduction

Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle It does so by inducing cancer-like phenotypes in the host cells it infects, the molecular and regulatory mechanisms involved remain poorly understood. Tretina et al BMC Genomics (2016) 17:128 transcription from a single defined nucleotide position, recent genome-wide studies favor a more intricate model that includes multiple promoters and start sites for most genes. This is a potentially significant source of transcriptome diversity [6]. We use the first published RNAseq dataset for T. parva, as well as a variety of bioinformatics methods to predict cis regulatory motifs in T. parva and other piroplasmids, and investigate the sequence and evolution of genomic motifs that regulate gene expression

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Results

Conclusion