Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein–DNA complexes

Naomi Yamada, Matthew J Rossi, Nina Farrell, B Franklin Pugh, and Shaun Mahony

Nucleic Acids Research, gkaa618,

This article describes a new approach to characterizing the spatial organization of protein-DNA complexes using collections of ChIP-exo data. The approach takes advantage of a unique aspect of the high-resolution ChIP-exo assay; the shape of the sequenced read profiles generated by ChIP-exo at individual binding sites are reflective of the underlying protein-DNA crosslinking events. Performing ChIP-exo on different subunits within a given regulatory complex results in experimental profiles that contain subtle differences in shape and magnitude, dependent on the position of the subunit within the complex. The authors can characterize a given regulatory complex’s protein-DNA crosslinking profiles by simultaneously aligning ChIP-exo data from multiple protein subunits within the complex and across multiple binding regions. They can estimate the positions and relative strengths of individual protein-DNA crosslinking events within the aligned crosslinking profiles.

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