# High-throughput engineering of combinatorial chromatin signals and epigenetic cellular memory

> **NIH NIH K01** · STANFORD UNIVERSITY · 2024 · $23,842

## Abstract

PROJECT SUMMARY/ABSTRACT
A major frontier of genomic medicine is to convert annotations of disease-associated variants
and gene expression states into actionable therapeutic targets. Genomic sequence editing by
CRISPR/Cas has garnered heightened interest as potential therapeutics, but still carries risks of
off-target mutagenicity, and is less effective at targeting cis-regulatory elements, where the
majority of disease-associated variants reside. A conceptual alternative to DNA sequence
editing is to deliver a brief pulse of a synthetic therapeutic that can trigger memorized silencing
of target promoters and enhancers in a "hit-and-run" strategy, bypassing concerns of
mutagenicity associated with DNA sequence editing, and immunogenicity associated with
constitutive expression of CRISPR/Cas components. In practice, engineering sustained
epigenetic transcriptional silencing has had mixed success, but recent efforts demonstrate
that constructing specific combinations of chromatin signals -- broadly encompassing cis-
regulatory elements, regulatory protein complexes, and covalent chromatin modifications --
can be critical for success. However, existing tools for manipulating chromatin signals at high
throughput are limited in combinatorial capacity. This proposal builds the knowledge base and
generalizable CRISPR/Cas tools to overcome such limitations to enable systematic engineering
of epigenetic silencing memory across genomic loci in human cells. The results will pave the
way for future epigenetic therapeutics that expand the directly targetable portion of the human
genome, including cis-regulatory elements that can be highly specific with respect to cell types
and disease pathophysiology. To achieve these objectives, I am proposing to train in
CRISPR/Cas synthetic biology, functional genomics, single-cell methods and neurogenetics.
This training will be mentored by a co-mentorhsip team consisting of Dr. Luke Gilbert (UCSF,
Innovative Genomics Institute, and Arc Institute), Dr. Howard Chang (Stanford) and Dr. Thomas
Montine (Stanford), each providing critical intellectual and physical resources for specific areas
proposed in the training plan and my career development. My career goal is to conduct research
at the forefront of genome regulation and genomic medicine as an academic principle
investigator.

## Key facts

- **NIH application ID:** 10896455
- **Project number:** 5K01HG012789-02
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Chris Chuan Shu Hsiung
- **Activity code:** K01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $23,842
- **Award type:** 5
- **Project period:** 2023-08-01 → 2024-10-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10896455

## Citation

> US National Institutes of Health, RePORTER application 10896455, High-throughput engineering of combinatorial chromatin signals and epigenetic cellular memory (5K01HG012789-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10896455. Licensed CC0.

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