Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms
Laura E. McKnight, Johnathan G. Crandall, Thomas B. Bailey, Orion GB Banks, Kona N. Orlandi, Vi N. Truong, Drake A. Donovan, Grace L. Waddell, Elizabeth T. Wiles, Scott D. Hansen, Eric U. Selker, Jeffrey N. McKnight
Abstract
MNase-seq (micrococcal nuclease sequencing) is used to map nucleosome positions in eukaryotic genomes to study the relationship between chromatin structure and DNA-dependent processes. Current protocols require at least two days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for S. cerevisiae and other fungi which takes only three hours. Modified protocols were developed for wild fungi and mammalian cells. This method for rapidly producing sequencing-ready nucleosome footprints from several organisms makes MNase-seq faster and easier, with less chemical waste.