Mapping the nucleosome state is most commonly done by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Crosslinked chromatin is fragmented, either mechanically or by MNase, and then incubated with antibody against a modification of interest. DNA fragments bound to the antibody are then extracted, sequenced, and mapped to the genome. The resulting occupancy map identifies genomic regions that are occupied by nucleosomes carrying the target modification. The accuracy of these assays depends on the quality of the antibody, its affinity for the target epitope, and cross-specificity to other epitopes (Egelhofer et al. 2011; Fuchs et al. 2011). Low affinity leads to low yields and a poor signal-to-background ratio. Cross-specificity can bias the results in a misleading manner, especially if the target modification state is rare compared to the off-target modification. The spatial precision depends on the fragmentation protocol, with larger fragments leading to a more spatially diffuse signal.
