A low-input compatible, end-to-end kitted HiChIP workflow for concurrent analyses of transcriptional
protein binding and chromatin interactions toward a mechanistic understanding of gene regulation
Arima Genomics
Project Summary/Abstract
Precise regulation of gene expression is paramount to establishing cellular identities, and mis-regulation of genes
causes human disease. Cells regulate gene expression using regulatory elements (REs), short DNA sequences
embedded throughout the genome, who are bound by transcriptional proteins to facilitate their regulatory
function. Molecular mapping tools, such as Chromatin immunoprecipitation and next gen sequencing (ChIP-
seq), produce “maps” of REs along the genome and have been a ubiquitous approach towards understand gene
regulation and define cell types and states based on unique RE signatures. However, these locations of REs are
only understood in context of a linear genome. In reality, REs execute their gene control within a three
dimensional (3D) genome. Therefore to truly understand gene regulation – gene regulation must be mapped in
3D. Indeed, high throughput chromatin interaction capture (HiC) was developed to produce 3D interaction maps
of all 3 billion bases in the human genome. HiC has facilitated discovery of several fundamental principles DNA
folding in 3D, including cases where DNA mis-folding contributes to disease. However, HiC does measure
transcriptional protein binding, nor whether a chromatin interaction is regulatory, thus having limited utility in
advancing our understanding 3D gene regulation. Recently, novel approaches attempt to combine the molecular
steps of ChIP-seq and chromatin interaction capture to measure transcriptional protein binding and mediated
chromatin interactions in a single assay. However these approaches, termed ChIA-PET and HiChIP, do not
efficiently capture chromatin interactions or transcriptional protein binding, respectively. Therefore, there is dire
need for improve methods that truly facilitate mapping of gene regulation in 3D.
We satisfy this unmet need via our highly optimized, first generation HiChIP solution, Arima-HiChIP (A-HiChIP),
that demonstrates efficient and reproducible mapping of transcriptional protein binding and chromatin
interactions in cell lines, with higher cellular inputs and a limited set of transcriptional proteins. Our team has
unmatchable expertise in the science of chromatin interaction capture and its commercialization. First, we
commercialized Arima-HiC kits in 2018 for studying general principles of chromatin interactions and generated
$1.2M in revenue in the 1st year of commercialization and $2M in revenue in the 2nd year, with 500+ customers,
and 100% growth from 2018 to 2019. Based on VOC analytics, we shifted our focus to develop a more relatable
product to the gene regulation market – A-HiChIP - that customers wanted and that represented a larger market
opportunity. Indeed, after our self-funded phase-1 R&D and commercial developments, we launched our first
generation HiChIP solution into the market and have seen remarkable success – measured by HiChIP growing
from 19% to 40% of our revenue contributions, increased quality of revenue, and traction with KOLs, large
consortia, and COVID research. However, these kits are limited in terms of the capabilities – they are not robust
to a range of transcriptional proteins, they are not optimized towards tissue samples, and they are not optimized
towards lower sample input quantities. To enable broader adoption and discovery, we have shown the
development towards our second-generation A-HiChIP solution, with advancement towards low sample inputs,
tissues, and a broader range of transcriptional proteins. We validate the technology on internal samples provided
by academic collaborators and externally in customer hands via prototype beta kits.
As part of this direct-2-phase II program, we propose to further develop our technology into truly robust, low input
compatible, end-to-end kitted HiChIP solution for concurrent analysis of transcriptional protein binding and
chromatin interactions in tissue samples and across a host of important transcriptional proteins. We also propose
rigorous and essential product development experiments, to ensure commercialization of a robust, premium-
performance kit-based product that is optimally integrated into the ecosystem. Upon successful completion of
the technical and commercial developments in Aims 1 & 2, we propose to benchmark and validate the our next-
generation HiChIP solution through collaboration and prototype (beta) kit and bioinformatics evaluations with key
opinion leaders (KOLs) across customer segments.
