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 ChIP-seq, ChIA-PET, PLAC-seq, and HiChIP. These methods all require high amounts of starting material (0.5M – 100M cells) and sequencing at high depth (a minimum of 150M reads per sample), 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 100,000 cells and 12M sequencing reads per sample. Activated transposase generates fragment libraries with extremely low background signal that are easily interpreted with minimal computational processing. This permits cost-effective protein-centric 3D genome profiling in systems previously unmeasurable, including primary cells and human tissue samples. We validated HiCuT method for two different proteins, CTCF and RNA polymerase 2 in GM12878 cells. Next, we performed HiCuT on primary skin cells with an anti H3K27ac antibody and identified previously validated long-range chromatin interactions. Importantly, the high resolution generated by HiCuT permitted annotation of previously identified single nucleotide polymorphisms (SNPs) in skin disease to potential target genes. Thus, HiCuT will permit protein-centric 3-D genome binding assessment in rare cell populations that were not feasible previously, including primary cells, human tissue samples, and personalized epigenomics.