# Editing CG and non-CG DNA methylation to identify genomic elements that regulate gene expression

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $403,750

## Abstract

PROJECT SUMMARY / ABSTRACT
A long-standing goal in biology is to define the relationship between genotype and phenotype. A major
surprise of the human genome project was that the human genome encodes so few genes despite the
complexity of cell types that compose for example, the human brain. As such it is assumed that
combinatorial gene expression programs are key for specifying the function of specialized cell types such
as neurons. Cell type specific gene expression programs therefore must be encoded by cis- and trans-
non-coding regulatory DNA elements whose function is regulated by the epigenetic code and key proteins
such as transcription factors. Elucidating how non-coding regulatory elements function to program cells will
transform our understanding of human biology, development and disease.
CRISPR/dCas9 technologies enable us to move beyond correlative studies, by editing the epigenome and
determining the direct effect of epigenetic alterations on gene expression. We have created a new
epigenetic editing functional genomics approach that we have named CRISPRoff. CRISPRoff robustly and
specifically writes CpG DNA methylation (5mC) and repressive histone modifications to target loci. We are
proposing to use CRISPRoff to map all genomic regulatory elements that are regulated by 5mC across an
entire human chromosome. In the proposed experiments we will use perturb-seq, which combines pooled
CRISPR screens with a single cell transcriptome readout, to directly measure how deposition of 5mC by
CRISPRoff across an entire chromosome modulates gene expression. This approach will identify genetic
regulatory elements key for induced pluripotent stem cells and neurons, a key step to understanding how
tissue-specific gene expression is controlled. Our proposed research will serve to demonstrate the utility of
this approach and motivate extending this approach to map gene regulatory elements across the entire
human genome. The results of the proposed research will serve as a fundamental resource and roadmap
for a broad community of biomedical scientists and greatly inform our understanding of human biology and
disease.

## Key facts

- **NIH application ID:** 10487529
- **Project number:** 5R01HG012227-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Hani Goodarzi
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $403,750
- **Award type:** 5
- **Project period:** 2021-09-10 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10487529

## Citation

> US National Institutes of Health, RePORTER application 10487529, Editing CG and non-CG DNA methylation to identify genomic elements that regulate gene expression (5R01HG012227-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10487529. Licensed CC0.

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