Accurate and Reproducible Genome Conformation Analyses

Combining proximity ligation with NGS for high resolution, genome-wide mapping of chromatin interactions

The Arima-HiC Kit is a highly simplified and robust protocol that streamlines Hi-C to a 6 hour workflow followed by library prep and next-generation sequencing. The Arima-HiC Kit empowers researchers to leverage Hi-C technology to perform genome-wide and targeted identification of promoter-enhancer interactions, link non-coding disease-associated variants to target promoters, and uncover how perturbations in genome conformation impact gene regulation in disease contexts.

  • Proven performance—greater accuracy of chromatin loop and topological domain detection even at reduced sequencing depth
  • Fast and user-friendly workflow—rapid 6 hour Hi-C workflow
  • Assured quality—rapid and easy library QC steps that accurately predict library quality, ensuring sequencing success
  • Flexible input requirements—Support for a broad range of sample types and an optimized protocol for low sample input

Hi-C for Conformation Studies

The three-dimensional (3D) organization of chromatin is a critical regulator of genome function across eukaryotes and is mediated by physical interactions between genomic loci that may be separated by a great distance along the linear genome. For example, millions of putative cis-regulatory elements have been identified, such as enhancers, with a great number of these found in intergenic regions thousands of kilobases away in linear sequence from neighboring genes. To obtain a more complete understanding of gene regulation, it is important to determine the 3D genome conformation and utilize this information to uncover the structural framework by which DNA chemical modifications, histone modifications, and chromatin binding proteins cooperate to orchestrate transcriptional regulation.

Hi-C is a proximity ligation method that captures long-range chromatin interactions across the genome, enabling researchers to uncover genome organizational structures such as chromatin compartments, topological domains (TADs), and chromatin loops. These structures all play important roles in gene regulation, such as providing a structural framework that confines local gene regulatory mechanisms and by providing a physical link between enhancers and their target genes – an integral component to the epigenetic mechanisms that regulate transcription.

By enabling genome-wide and targeted identification of 3D genome structures and promoter-enhancer looping, Hi-C has emerged as a powerful tool for refining our understanding of gene regulation within the 3D context of the genome and is widely used today in a variety of research areas and large-scale 3D genome mapping projects.

Comprehensive Arima-HiC Workflow

Arima-HiC Prep

Chromosomes in Nucleus
Rapid 6 hour Protocol
  • Chromatin cross-linking
  • Digest crosslinked chromatin
  • Ligation
  • QC Check

Library Prep

Paired-End Reads
Pre-validated library prep protocols
  • KAPA HyperPrep (Preferred for Standard Input)
  • Swift Accel-NGS 2S Plus (Preferred for Low Input)
  • Illumina TruSeq
  • Other


DNA Sequencer
Optimized for next generation sequencers
  • Illumina NovaSeq
  • Illumina HiSeq
  • Illumina NextSeq
  • Illumina MiSeq
  • BGI-Seq

Data Analysis

Conformation Analysis
Powerful analysis with open source tools
  • Arima Genomics Mapping Pipeline
  • Juicer
  • HiC-Pro
  • HiCUP
  • HiC-Bench
  • Other

Interested in learning more?

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