Figure 8.

Comparison of expression patterns in subtelomeric and internal chromosomal regions. Displayed are expression curves of the top 100 genes with highest expression change rates. The genes were manually assigned to classes C1, C2, C3, C4, C5, and C6, which differ by their expression patterns. (a) Forty-two subtelomeric genes (position < 230 kb from the closest telomere). (b) Fifty-eight internal chromosomal region genes (>230 kb). Class C1 is over-represented in subtelomeric genes: only a single member of the C1 pattern (MAL7P1.58) is found amongst the top 100 intrachromosomal genes. By contrast, the C2 expression pattern is under-represented in subtelomeric genes, with PFI0160w being the only member of C2 in the subtelomeric proportion, whereas C2 is a rather common expression pattern in central chromosome parts. The class C6 expression pattern is solely observed in the subtelomeric areas. Similarly, the related pattern of class C5 is observed predominantly among subtelomeric genes. Class C3 and C4 patterns are present in both regions of the chromosomes, subtelomeric and central areas (see also the genome-wide up-regulation displayed, for example, in Figure 4c). Note the fast disappearance of the RNA in class C6 at the transition from ring to trophozoite stage, which might indicate unstable transcripts or active removal of message, whereas, for example, class C1 contains more stable mRNA as suggested by a low degree of down-regulation (approximately 25 h; see also the Discussion). Lists of genes are provided in Additional data files 2 and 3.