# Determinants of Persistence in Epigenetic Editing

> **NIH NIH R21** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2020 · $187,240

## Abstract

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PROJECT SUMMARY
Precise regulation of gene expression is critical for development and cell identity. Misregulation
of this tightly controlled process can lead to disease such as cancer or neurological disorders.
Distinct epigenetic marks (DNA methylation and post-translational histone modifications) have
been associated with expressed or silenced genes as well as with regulatory elements in the
genome. Traditionally, drugs (e.g., decitabine, vorinostat) are used to induce epigenetic
changes in an untargeted manner and thus can alter epigenome signatures throughout the
genome. With the RNA-guided Cas9/CRISPR complex, we now have a tool that can easily and
precisely target a 20-bp sequence in the genome. We and others have developed targeted
epigenetic regulators that are based on fusions of effector domains to the catalytically inactive
dCas9. We have shown that dCas9 fused to various epigenetic effector domains (epi-dCas9)
can regulate transcription in a targeted manner. However, two major challenges have to be
overcome before we can use these tools efficiently: 1) Efficiency of epigenetic regulators is
dependent on the genomic locations. Pre-existing chromatin environment and three-
dimensional interactions that make a target locus amenable to persistent targeted epigenome
editing are not yet understood. 2) The factors and pathways to efficiently achieve persistent
targeted gene silencing are not well defined. Clearly, a better understanding is needed of the
targetable epigenome that is amenable to persistent gene silencing and an understanding of the
pathway(s) to accommodate persistent gene silencing. We will gain these foundational
insights by determining promoter features amenable to persistent targeted gene
silencing by epi-dCas9 (Aim 1), and identifying pathway(s) required for persistent target
gene silencing using an innovative epi-dCas9/knockdown editing screening system (Aim
2). In the first Aim, we will test several epi-dCas9 fusions on 80 promoters representing different
expression levels and epigenetic states, then identify features that are permissive or resistive to
persistent silencing. In a parallel Aim, we will combine an epi-dCas9 repressor with a genome-
wide CRISPR/Cas9 screen to identify cellular genes involved in epigenetic persistence. Not only
will this information advance the capabilities of us and others to create targeted persistent
epigenetic changes for the study and treatment of disease, it will also provide fundamental
insights into the mechanistic steps required to transition from one epigenetic state to another.
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## Key facts

- **NIH application ID:** 9920184
- **Project number:** 5R21HG010559-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** DAVID J SEGAL
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $187,240
- **Award type:** 5
- **Project period:** 2019-04-23 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9920184

## Citation

> US National Institutes of Health, RePORTER application 9920184, Determinants of Persistence in Epigenetic Editing (5R21HG010559-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9920184. Licensed CC0.

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