# Spatiotemporal mapping of enhancer activity in developing frog embryos

> **NIH NIH R21** · UNIVERSITY OF CALIFORNIA-IRVINE · 2022 · $228,235

## Abstract

Project Summary:
All cell types in an organism share the same basic genetic information, yet they execute remarkably
diverse gene expression programs and behaviors. Much of this diversity is derived from cell type-specific
and condition-specific usage of gene-distal regulatory regions known as cis-regulatory modules (CRMs)
(also known as enhancers). Typical mammalian genomes contain hundreds of thousands of CRMs
distributed across large genomic distances that act collectively and collaboratively to produce differential
gene expression patterns of extreme complexity. At present, our understanding of the biological roles of
most of these CRMs remains limited. For instance, how are specific CRMs selected to regulate a given
gene's expression? How do different CRMs coordinate and activate various target genes in a spatially
and temporally regulated manner? Our lack of understanding is in large part due to current limitations in
delivering simultaneous experimental measurements of the activities of large numbers of CRMs during
animal development. The major goal of this proposal is the successful use of Xenopus gastrula-stage
embryos as a model system for quantifying CRM activities involved in delivering precise spatiotemporal
expression patterns of target genes. While CRM activities are to be assayed at a genome-wide level,
their associated gene regulatory mechanisms would be determined with single-cell resolution. Applying
advanced computational biology algorithms to that data will deliver mapping of CRM activities sufficient
to infer the TFs and associated signaling processes involved in regulation of differential cell states in
gastrulae at single-cell resolution. We propose to address two specific aims. First, we will apply a modified
STARR-seq approach to identify CRMs that regulate spatiotemporal gene expression patterns in gastrula
embryos. We plan to mutate potential TF binding sites within CRMs to aid in identifying their biological
functions. Second, we will combine scRNA-seq with STARR-seq as a means of uncovering CRM-centric
gene regulatory structures critical for specifying cell states for every cell in gastrula-stage embryos. In
sum, we will use Xenopus tropicalis gastrula-stage embryos as the model system for generating a
system-level understanding of CRM activities in single cells because of the key phylogenetic position
amphibians occupy in the vertebrate evolutionary lineage. The approach proposed here would be much
more difficult to perform in mammals, because their embryos are not easily accessed for certain
necessary experimental manipulations, and because mammalian embryo availability is rate limiting for
some genomic work.

## Key facts

- **NIH application ID:** 10511083
- **Project number:** 1R21HD109696-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** Ken W.Y. Cho
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $228,235
- **Award type:** 1
- **Project period:** 2022-08-19 → 2024-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10511083

## Citation

> US National Institutes of Health, RePORTER application 10511083, Spatiotemporal mapping of enhancer activity in developing frog embryos (1R21HD109696-01). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10511083. Licensed CC0.

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