Assays for nucleosome positioning in yeast

Publisher Summary Positions of nucleosomes are defined translationally and rotationally. Translational positioning specifies where the histone core begins and ends along a DNA sequence. Rotational positioning refers to the orientation of a DNA helix relative to the histone core. Several techniques have been developed to map both the translational and rotational positioning of nucleosomes. These techniques utilize enzymes or chemicals that cleave nucleosomal and nonnucleosomal DNA differentially. Differential cleavage is largely because of the wrapping of DNA around the nucleosome core, which makes DNA in chromatin less accessible to cutting. In many cases, the mechanism of positioning is unclear. Experimental evidence indicates that nucleosome positioning can be directed by a DNA sequence and by DNA-binding proteins that position nucleosomes or generate nucleosome-free regions that influence positioning in adjacent sequences. This chapter discusses the methodologies that are used to assess nucleosome positioning in yeast.