Supplementary materials for PhD thesis “Transcriptional regulation of yir genes in Plasmodium yoelii yoelii infected erythrocytes”

<i>This dataset </i><i>comprises</i><i> the files contained on a CD-ROM which was attached to the thesis when it was </i><i>submitted</i><i> in 2006</i><i>. It was uploaded to ORDO in 2024 for preservation purposes.</i><i> </i><i>For more information, please refer to the thesis </i><i>Transcriptional regulation of yir genes in Plasmodium yoelii yoelii infected erythrocytes</i><i>.</i>In 1998, a large multi gene family was discovered in <i>Plasmodium vivax</i> (del Portillo et al., 1998). This multigene family was termed <i>vir</i>, and later studies showed that <i>vir</i> homologues existed in the three rodent malaria species, <i>Plasmodium chabaudi (cir), Plasmodium berghei (bir)</i> and <i>Plasmodium yoelii (yir)</i>. By 5x coverage sequencing of <i>Plasmodium yoelii</i> 17X, 838 <i>yir</i> genes were predicted (Carlton et al., 2002), making this the largest known multi gene family in <i>Plasmodium</i>. YIR proteins are expressed at the surface of infected erythrocytes (Cunningham et al., 2005), and therefore this family is thought to be involved in antigenic variation.<br><br>The aim of this thesis was to examine how <i>P.yoelii</i> regulates transcription of the <i>yir</i> family. The <i>yir</i> gene structure was verified experimentally, and phylogenetic analysis showed that <i>yir</i> genes could be divided into five supergroups consisting of <i>yir</i> genes with different sizes and subtelomeric localisation. In the blood stages, numerous <i>yir</i> genes were transcribed from all the supergroups in immunocompromised mice. However, a maximum of two <i>yir</i> genes were transcribed in single infected erythrocytes at the Schizont stage, which suggested strong silencing mechanisms. The transcriptional start and polyadenylation sites were identified experimentally, and it was found that both occurred at highly conserved motifs. In addition, the transcription initiation site was located close to an unusual and universally conserved triple-repeat motif, and it was found that all <i>yir</i> transcripts in two populations of parasites initiated downstream of this motif. Transfection experiments were performed in order to examine the role of this motif, but no solid conclusions could be drawn from these. Several alternative splicing events were detected in the <i>yir</i> 5<i>'</i>UTRs, and one of these led to exon 1 skipping of a <i>yir</i> gene. Through bioinformatic analysis of <i>yir</i> 5<i>'</i> intergenic regions, it was found that the UTR introns had a discrete distribution amongst the <i>yir</i> supergroups.