Identification of putative subtelomeric regions in the genome of Toxoplasma gondii

CARMONA SJ; DALMASSO MC; ANGEL SO; AGÜERO F

Oro Verde, Entre Rios

Congreso; 3er Congreso Argentino de Bioinformática y Biología Computacional (CAB2C); 2012

Asociacion Argentina de Bioinformatica y Biologia Computacional

Background Most eukaryotic chromosome ends are formed by telomeric repeats and subtelomeric regions, also called Telomeric Associated Sequences (TAS). TAS are patchworks of genes interspersed with repeated elements, and while these domains present similar arrangements in different species, their sequences are highly divergent. In addition, these regions present a particular nucleosomal composition and bind specific factors therefore producing a special kind of heterochromatin (Ottaviani et al 2008). In the currently available draft of the T. gondii genome, telomeres are not completely assembled, and chromosome ends have not been analyzed yet. Here we discuss some findings regarding T. gondii chromosome ends. Results All-vs-all pairwise sequence comparison of T. gondii chromosomes revealed the presence of a conserved region of approximately 25 to 30 Kbp at the ends of 9 of the 14 chromosomes in the parasite strain ME49, defined here as TgTAS-like. Sequence similarity among these regions is on average ~70%, they are highly conserved in other strains, but are unique to Toxoplasma, with no detectable similarity in other Apicomplexan parasites. The internal structure of these TgTAS-like sequences consist of 3 repetitive regions separated by high-complexity sequences that are depleted of genes, with the exception of one gene at their 3' end. To analyze potential compositional bias along the chromosome we performed a correspondence analysis (CA) of the trinucleotide composition observed in sliding windows of lengths 1K to 100K. The analysis showed a strong bias, with only 2 dimensions (the first and second principal coordinates of the CA) largely explaining the trinucleotide bias (>60%). TgTAS-like regions showed the highest trinucleotide compositional bias on the first principal coordinate (1PC) when using a window size of 30Kbp . This compositional bias is similar to that observed in other genomic fragments such as those containing centromeric sequences (Figure 1). We also found that 1PC is negatively correlated to gene density in the genome (Pearson's correlation coef. -0.445, p-value < 10^-16), ie genomic fragments with low 1PC values are gene-rich while high 1PC is associated to gene-depleted regions, such as TgTAS-like and centromeres. Finally ChIP-qPCR experiments showed that TgTAS-like sequences present a special nucleosomal composition, enriched in heterochromatin markers such as H4K20me1 and H2AX. Conclusions We identified a region encompassing ~ 30 Kb present in most of the Toxoplasma chromosomes, denominated TgTAS-like. They form a specialized heterochromatin, characterized by: i) a particular trinucleotide composition, ii) a special arrangement containing three satellite families, iii) depletion of coding sequences, and iv) enrichment in nucleosomes containing heterochromatin-like histone markers. In addition, TgTAS-like and the unique gene present at their 3' ends are Toxoplasma specific. Therefore, we proposed that TgTAS-like are the subtelomeric regions of T. gondii.Interestingly, these features allowed us to identify similar regions, not necessarily sub-telomeric, that might be functionally similar.