Centromere-Like Regions in the Budding Yeast Genome
Figure 4
(A) Comparison of CLRs and CENs. Average value refers to the fraction of CLRs or CENs located within 25 kb of a CEN or within 5 kb of an ARS, tRNA or retrotransposon. Mean intergenic indicates the average length of intergenic regions. Max AT represents the mean AT content of the most AT-rich 90-bp stretch of DNA. (B) CLRs can be separated from other genomic regions, using Discriminant Analysis (DA). Scores of CLRs (blue) and negative control regions (red) are plotted according to their discriminant function scores (Table 2). (C) Centromere proximity is a major contributor to variability among CLRs, as revealed by Principal Component Analysis (PCA). Scores of CEN-proximal (<25 kb, blue) and CEN-distal (>25 kb, red) CLRs are plotted relative to the first and second principal components (Table 3), along with a 95% confidence ellipse. (D) Conservation of CLR sequences among organisms with point CENs (blue), but not with fungi bearing regional CENs (black). Nucleotide blast (Blastn) was performed for 23 CLRs and 160 random intergenic regions. Mean BLAST scores are reported, with the percent of hits with a score over 45 (E<0.05) in parentheses. (E) Given our data and the confinement of CLR sequences to budding yeast bearing point centromeres, we proposed a modified version of the current model of centromere evolution (originally postulated in [1]), from regional to point CENs, to account for CLRs. CLRs would represent evolutionary remnants from regional CENs. Some AT-rich CEN repeats would have diverged but still retained the ability to bind Cse4 and other kinetochore proteins weakly, giving rise to the low-affinity CLRs observed in this study.