Discover active gene regulation interactionsApplication Note
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).
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
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