A shortcoming of the nuclease-based methods typically used for nucleosome mapping is imprecision in positioning data caused by variability in nuclease digestion of nucleosome ends. Several epigenomic methods have been developed which provide greater precision in mapping of DNA-bound factors, in some cases offering structural insights into DNA-protein complexes at a resolution that can be confirmed by comparison to crystal structures of the relevant factors. For example, extremely deep sequencing of nuclease- and transposase-susceptible genomic regions has proven to yield high resolution insights into nucleosome positioning and TF binding. This has been reported for DNase I digestions, where moderate depth mapping reveals nucleosome-depleted regulatory elements, but ultra-deep sequencing additionally reveals detailed footprints of certain transcription factor binding sites which can be reconciled with the pattern of protein-DNA contacts expected from crystal structures (Hesselberth et al. 2009). Similarly, deep sequencing of ATAC-seq libraries reveals transcription factor footprints and even exhibits 10.5-bp periodicity across nucleosomes (Buenrostro et al. 2013), potentially providing information on the rotational positioning of nucleosomes (e.g., where the DNA major groove faces toward the histones vs. toward the nucleoplasm).
