HiCuT: an efficient and low input method to identify protein-centric chromatin interactions

Protein-DNA interactions regulate gene expression, and some interactions occur over large distances, such that they are nearby in 3-D space but are separated by many nucleotides in the linear genome. These long-range chromatin loops are essential for gene regulation but remain difficult to interrogate. Methods to capture these chromatin interactions mediated by a specific protein factor include Hi-C sequencing coupled with chromatin immunoprecipitation-sequencing (ChIP-seq), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), proximity ligation-assisted ChIP-seq (PLAC-seq), and HiChIP. These methods all require high amounts of starting material (0.5M – 100M cells) , which limits their general use. Here, we describe Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT), an enzyme-based tagmentation strategy that provides efficient and high-resolution protein-centric chromatin mapping from as few as 5,000 cells. Thus, HiCuT will permit protein-centric 3-D genome binding assessment in rare cell populations that were previously not testable, including primary cells, human tissue samples, and personalized epigenomics. Overall design: HiCuT assay on GM12878 and primary Keratinocytes