Genome-wide rotational and translational phasing of nucleosomes with human transcription factors [ChIP-exo]

When Benzonase cleavages are analyzed in the context of TF binding sites, we determine whether the TF motif has a prefer orientation on the nucleosome surface. When this assay is coupled to chromatin immunoprecipitation (ChIP) of histones, histone variants, and modifications, we find evidence for transcription-linked subnucleosomal structures, some of which may be related to hexasomes and half/split-nucleosomes. Benzonase-seq offers a robust and ultra-high resolution method to map the translational and rotational setting of DNA elements on the nucleosome surface, and provides a means to probe subnucleosomal structures.

Benzonase-seq may be useful for probing the pioneering potential of transcription factors.