Characterization of the Yeast Telomere Nucleoprotein Core

Abstract

At the core of Saccharomyces cerevisiae telomeres is an array of tandem telomeric DNA repeats bound site-specifically by multiple Rap1 molecules. There, Rap1 orchestrates the binding of additional telomere-associated proteins and negatively regulates both telomere fusion and length homeostasis. Using electron microscopy, viscosity, and light scattering measurements, we show that purified Rap1 is a monomer in solution that adopts a ringlike or C shape with a central cavity. Rap1 could orchestrate telomere function by binding multiple telomere array sites through either cooperative or independent mechanisms. To determine the mechanism, we analyze the distribution of Rap1 monomers on defined telomeric DNA arrays. This analysis clearly indicates that Rap1 binds independently to each non-overlapping site in an array, regardless of the spacing between sites, the total number of sites, the affinity of the sites for Rap1, and over a large concentration range. Previous experiments have not clearly separated the effects of affinity from repeat spacing on telomere function. We clarify these results by testing in vivo the function of defined telomere arrays containing the same Rap1 binding site separated by spacings that were previously defined as low or high activity. We find that Rap1 binding affinity in vitro correlates with the ability of telo-meric repeat arrays to regulate telomere length in vivo. We suggest that Rap1 binding to multiple sites in a telomere array does not, by itself, promote formation of a more energetically stabile complex. Telomeres are specialized chromatin domains that control numerous DNA processes occurring at the termini of linear eukaryotic chromosomes. The telomere nucleoprotein complex regulates transcription of nearby genes, telomere duplication through semi-conservative DNA replication, de novo extension of telomere DNA by telomerase, telomere recombi-nation, and chromosome stability. In the absence of proper telomere structure, these processes become deregulated, and cells normally halt the cell cycle; continued cell division can lead to telomere fusions and other aberrant DNA recombina