Genetic and Genomic Analysis of the AT-Rich Centromere DNA Element II of Saccharomyces cerevisiae

Abstract

Centromere DNA element II (CDEII) of budding yeast centromeres is an AT-rich sequence essential for centromere (CEN) function. Sequence analysis of Saccharomyces cerevisiae CDEIIs revealed that A 5-7 /T 5-7 tracts are statistically overrepresented at the expense of AA/TT and alternating AT. To test the hypothesis that this nonrandom sequence organization is functionally important, a CEN library in which the CDEII sequences were randomized was generated. The library was screened for functional and nonfunctional members following centromere replacement in vivo. Functional CENs contained CDEIIs with the highly biased A n /T n run distribution of native centromeres, while nonfunctional CDEIIs resembled those picked from the library at random. Run content, defined as the fraction of residues present in runs of four or more nucleotides, of the functional and nonfunctional CDEII populations differed significantly (P , 0.001). Computer searches of the genome for regions with an A 1 T content comparable to CDEIIs revealed that such loci are not unique to centromeres, but for 14 of the 16 chromosomes the AT-rich locus with the highest A n$4 1 T n$4 run content was the centromere. Thus, the distinctive and nonrandom sequence organization of CDEII is important for centromere function and possesses informational content that could contribute to the determination of centromere identity.

Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs

“…This relative AT-richness distinguishes the SSR from the remainder of the genome where it is 35% [6]. This physical characteristic may facilitate weaker binding of the two strands during either transcription or replication processes, and is classically found in the non-coding regions with a structural role such as centromeres or replication origins [16,17]. The whole of these features shows that the general structure of this region is highly conserved among the 15 species studied here.…”

Rapid Evolution of Yeast Centromeres in the Absence of Drive

“…CDEII wraps around the centromere-specific histone Cse4; this binding is analogous to that between mammalian centromeric repeats and CENPA (the mammalian homolog of Cse4), although in the case of yeast only a single nucleosome is formed for each centromere (Sullivan et al 2001). CDEIIs from different chromosomes are highly dissimilar (up to 60% differences among those sequenced here) yet functionally interchangeable (Clarke and Carbon 1983), indicating that the binding of CDEII to the centromere-specific histone Cse4 is not sequence specific, although changes in the length, AT content, and pattern of runs of A's and T's can disrupt centromere function, perhaps by altering DNA bendability or flexibility (Baker and Rogers 2005). CDEII diverges more than twice as fast as the two binding sites ( Figure 4 and Table 1; G-test, P EF ¼ 0.001, P EC ¼ 2 3 10 À11 ), which do not differ significantly from each other (P .…”

“…Moreover, a 9-fold increase in the mutability of C/G would also produce a 1.8-fold increase in the rate of divergence at equilibrium (Haddrill et al 2005). On the other hand, the A/T bias appears to be functionally important (Baker and Rogers 2005), and it could be maintained purely by selection, without a mutation bias. In this case there would be purifying selection against mutations to C or G, and the actual mutation rate at CDEII would be even higher than the divergence rate we observe.…”

Tetrameric organization of vertebrate centromeric nucleosomes

“…In metazoans, centromeric DNA alone is insufficient to dictate centromere location, as evidenced by the formation of satellite-free neocentromeres (2,3). That a common epigenetic identity prevails can be deduced from a number of studies spanning evolutionary, biochemical, cytological, genetic, and genomic methods (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22), all of which pinpoint CENH3 as the key epigenetic marker for active centromeres in eukaryotes.…”