Dovetail® HiChIP MNase Kit

The Dovetail™ HiChIP MNase Kit combines the benefits of ChIP-seq with Hi-C, a proximity ligation method that captures long-range interactions using standard Illumina paired-end sequencing, allowing researchers to query the conformation of protein-driven chromatin mediated by specific proteins of interest.

Key Benefits of HiChIP:

• Capture ChIP-seq and Hi-C data together in a single library.
• Map chromatin interactions at the nucleosome level of resolution..

The unique combination of the Dovetail™ Micro-C proximity ligation assay with the Dovetail HiChIP approach allows the use of micrococcal nuclease (MNase) to fragment chromatin uniformly and without sequence bias prior to proximity ligation, eliminating the need for meticulous sonication procedures and offering maximum resolution (down to mononucleosome size) of chromatin interactions.

The enrichment of protein-targeted chromatin features enables the generation of high-resolution contact maps with less read depth. Compared to a high-resolution restriction enzyme-based Hi-C, Dovetail HiChIP data enables visualization of higher-order chromatin features, such as loops and chromatin interactions, at a fraction of the reading depth, which generates significant savings in sequencing costs.

This guide will guide you step by step on how to QA your HiChIP library, how to interrelate QA results, and how to call and plot meaningful interactions. If you don't already have a sequenced HiChIP library and want to get familiar with the data, you can download HiChIP sequence libraries from our publicly available datasets.

The quality control process begins with aligning reads to a reference genome and then retains high-quality mapped reads. From there, the mapped data will be used to generate a pairs file with pairtools, which categorizes pairs by read type and insertion distance, this step marks and removes PCR duplicates. Once the pairs are ranked, the counts for each class are added and reported.

If this is your first time following this tutorial, check the Before You Begin page first.

Introduction to HiChIP Technology