Higher-order structure of Saccharomyces cerevisiae chromatin.

Abstract

We have developed a method for partially purifying chromatin from Saccharomyces cerevisiae (baker's yeast) to a level suitable for studies of its higher-order folding. This has required the use of yeast strains that are free of the ubiquitous yeast "killer" virus. Results from dynamic light scattering, electron microscopy, and x-ray diffraction show that the yeast chromatin undergoes a cation-dependent folding into 30-nm filaments that resemble those characteristic of higher-cell chromatin; moreover, the packing of nucleosomes within the yeast 30-nm filaments is similar to that of higher cells. These results imply that yeast has a protein or protein domain that serves the role of the histone H1 found in higher cells; physical and genetic studies of the yeast activity could help elucidate the structure and function of Hi. Images of the yeast 30-nm filaments can be used to test crossed-linker models for 30-nm filament structure.We are interested in using the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe as model organisms in studies of eukaryotic chromatin structure, principally for two reasons. (i) We would like to use yeast genetics to identify and study the proteins necessary for the highest levels of chromosome folding. (ii) Although the manner in which nucleosomes are packaged together in 30-nm chromatin filaments is known approximately, the connectivity of the structure is not known (1). S. cerevisiae and neuronal cells have approximately no linker DNA (2-4), so studies of the higher-order folding of such chromatin could place strong constraints on possible connectivities. Previous studies of neuronal chromatin have shown it to fold into a higher-order structure that appears similar to the 30-nm filaments of higher cells (3, 4). One would like to extend these results by using methods such as electron microscopy of negatively stained samples or x-ray diffraction to study the packing of nucleosomes within the neuronal chromatin 30-nm filaments. However, because it has not been possible to isolate long oligomers of this neuronal chromatin, no such studies have been carried out. One might hope that yeast chromatin would present no such difficulty.One must first address the question: are the folded states of yeast chromatin similar to those of higher cells? The sequences of the four core histones (particularly H3 and H4) of both yeasts are quite homologous to those of higher eukaryotes (5), and nuclease digestion experiments reveal a similar pattern of DNA protection except for subtle differences near the ends of the nucleosomal DNA (6). In the absence offurther information it is reasonable to suppose that yeast nucleosomes will be similar in size and shape to those of higher cells. Surprisingly, it is not known whether this similarity extends to higher levels of chromosome structure. One study reported electron microscopic evidence for the existence of a 30-nm filament-like state of S. cerevisiae chromatin (7), but this has remained a matter of debate (8). A protein homologous to higher-c...

Bcl-2 family members inhibit oxidative stress-induced programmed cell death in Saccharomyces cerevisiae

“…In addition, S. cerevisiae chromatin structure has been reported to have little or no linker DNA between nucleosomes, which would preclude ladder formation [49]. The ability of yeast to die in an apoptotic-like manner is consistent with the idea that programmed cell death was in place before the divergence of yeast and metazoans.…”

“…Again, these data draw parallels to observations of PCD in animal cells where the defining characteristics include nuclear pyknosis and DNA fragmentation. These parallels are significantly furthered by the recent report that yeast cells harbor a cysteine protease distantly related to mammalian caspases, designated metacaspases [49]. The yeast metacaspase not only has structural, but also functional homology to mammalian caspases.…”

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

“…Nuclease fragmentation and isolation of native chromatin fibers results in nucleosome chains coated with nonhistone "husks" (24) that obscure transmission electron microscopy imaging (Fig. 1D).…”

Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast.

“…Although the budding yeast is thought to lack HI histone (Perez-Ortin et al 1989), a functional HI homolog was demonstrated recently (Lowary and Widom 1989). In addition, active genes in yeast and higher eukaryotes display similar functional features, i.e., enhanced sensitivity to singlestranded endonuclease SI and DNase I at sites flanking the active genes (for reviews, see Weintraub 1985;PerezOrtin 1989), indicating an alteration of nucleosomal organization in the promoter and coding regions upon gene activation.…”

“…The budding yeast Saccharomyces cerevisiae and higher eukaryotes share several common features of chromatin structure, including nucleosomal organization, folding of chromatin into higher-order structures, as well as the conservation observed for transcriptional machinery (Weintraub 1985;Guarente 1988;Lowary and Widom 1989;Perez-Ortin et al 1989). Although the budding yeast is thought to lack HI histone (Perez-Ortin et al 1989), a functional HI homolog was demonstrated recently (Lowary and Widom 1989).…”