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

Eukaryotic DNA is wrapped around a complex of histones, such that one face of the helix is accessible, and the other is buried. Sliding and rotating DNA by 5 bp in either direction reverses this polarity. This has substantial ramifications for regulating transcription factor (TF) binding. Yet, there does not exist a method to measure the rotational setting of DNA on nucleosomes in vivo and on a genomic scale. We developed Benzonase-seq, Benzonase cleaves and marks the accessible rotationally exposed DNA surface, in addition to marking linker regions between nucleosomes. Further, Benzonase robustly maps nucleosomes in CpG-rich mammalian promoters compared, which has been challenging for the commonly used micrococcal nuclease (MNase). 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.