Discover active gene regulation interactions. The easy-to-use and reproducible Arima-HiChIP approach streamlines the HiChIP protocol via a 2-day workflow and is optimized for efficient capture of chromatin looping (3D) and ChIP enrichment (1D) data. It facilitates broad and easy access to the powerful HiChIP technology.
- Discovery of active gene regulatory interactions at high resolution
- Compatible with a range of commercially available library prep kits
- Demonstrated differential loop calling between sample types
- Robust across cell types and protein targets
- Reduced sequencing costs
- 2 day workflow with simple protocol for first time-users
The Arima-HiChIP protocol is a reproducible and simplified protocol for identifying long-range genomic contacts mediated by proteins. HiChIP combines Hi-C and chromatin immunoprecipitation with antibodies against a protein of interest to enrich for interactions mediated by this protein. As a targeted approach HiChIP has the advantage of requiring less sequencing compared to Hi-C. Whereas Hi-C can potentially detect all types of chromatin interactions, Arima HiChIP targeting H3K27ac or H3K4me, using Arima validated antibodies, is specific for interactions linking active regulatory domains (see application note).
Arima-HiChIP Library Preparation
Arima-HiChIP is a 2-day protocol that results in proximally-ligated DNA that was associated with an immunoprecipitated protein of interest. This enriched DNA is then prepared as an Arima-HiChIP library in 1-day using a pre-validated commercially available library prep kit, namely the Accel-NGS 2S Plus DNA Library Kit from Swift Biosciences. After library prep, the resulting Arima-HiChIP libraries are sequenced in paired-end mode via Illumina next generation sequencers.
Fig.1. Arima-HiChIP Experimental Workflow
- Discovery of active gene regulatory interactions
- Mapping of CTCF-mediated genome folding using H3K27ac and H3K4me3
- Studies of promoter-enhancer communication
Introduction to Arima-HiChip
- Chenfu Shi, Magnus Rattray, Gisela Orozco (2020) HiChIP-Peaks: A HiChIP peak calling algorithm. Bioinformatics, 36(12):3625–3631