Does DNA sequence matter for nucleosome positioning in vivo?
Nucleosome formation is a first step towards packaging genomic DNA into chromosomes. Nucleosomes are formed by wrapping 147 base pairs of DNA in a superhelix around a spool of eight histone proteins. It is reasonable to assume that formation of single nucleosomes in vitro is primarily determined by DNA sequence: it costs less elastic energy to wrap a flexible DNA polymer around the histone octamer, and more if the polymer is rigid. However, it is unclear to which extent this effect is important in living cells, which have evolved chromatin remodeling enzymes to actively reposition nucleosomes. In addition, nucleosome positioning on genome-length DNA sequences is strongly affected by steric exclusion – multiple nucleosomes have to form simultaneously without overlap, creating regular arrays. At the same time, our recent analysis of the changes in chromatin structure that accompany addition of glucose to starved yeast cells (in collaboration with James Broach) reveals that correlation be
