# Gene expression and regulation in C. elegans with single cell resolution

> **NIH NIH R01** · UNIVERSITY OF WASHINGTON · 2021 · $510,309

## Abstract

Abstract
The nematode C. elegans is unique among model organisms in having a defined lineage
and known connections for all its 302 neurons. The genome sequence was completed
more than 20 years ago, but knowing which genes in the genome are used in exactly
which cells and what transcription factors are controlling that expression remains a major
challenge. We have successfully applied single cell- (sc-)RNA-seq methods to one
larval stage and three embryonic stages to measure the RNA content of individual cells
across the whole animal. We also have preliminary data that indicates that we can
assay chromatin accessibility at the single cell level using the assay for transposase
accessible chromatin (ATAC-seq). We now propose to collect both sc-RNA-seq and
ATAC-seq data at multiple stages to determine the gene expression patterns of each cell
in the worm and the active regulatory sequence throughout the entire life cycle of C.
elegans. In turn we will use the combined data sets along with chromatin-
immunoprecipitation- (ChIP-) seq data to impute what transcription factors are controlling
expression of each gene in the genome in every cell and what regulatory sequences
these transcription factors recognize. The results will provide a valuable resource to
scientists studying the worm and addresses a major outstanding question in the
molecular biology of development. In addition, these data sets, from an animal with a
“ground truth” should serve as a platform for methods development in the single cell
field.

## Key facts

- **NIH application ID:** 10149376
- **Project number:** 5R01HG010478-03
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** ROBERT H WATERSTON
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $510,309
- **Award type:** 5
- **Project period:** 2019-07-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10149376

## Citation

> US National Institutes of Health, RePORTER application 10149376, Gene expression and regulation in C. elegans with single cell resolution (5R01HG010478-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10149376. Licensed CC0.

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