Microarray Mapping of Nucleosome Position
Brian Spetman, Sarah Lueking, Brooke Roberts and Jonathan H. Dennis
from: Epigenetics: A Reference Manual (Edited by: Jeffrey M. Craig and Nicholas C. Wong). Caister Academic Press, U.K. (2011)
The location and density of nucleosomes in the eukaryotic genome plays a role in regulating nuclear processes including transcription, replication, recombination, and repair. Microarray mapping of nucleosomally protected DNA has emerged as a powerful, cost-effective, high-throughput method to analyze the relationship between nucleosome position and genomic regulation. In this chapter we discuss experimental considerations such as sample preparation and microarray design. In addition, two procedures are detailed: (1) Formaldehyde Crosslink and Harvest Cells, Isolate Nuclei, and MNase cut chromatin, and (2) Isolation of mononucleosomally protected DNA and fluorescent labeling of DNA for microarray hybridization. With the information specified in this chapter, most any laboratory equipped for molecular biology with institutional or commercial access to microarray facilities should be should be able to map nucleosome position and occupancy read more ...