# Molecular timekeeping and temporal cell fate specification in C. elegans

> **NIH NIH R01** · COLD SPRING HARBOR LABORATORY · 2024 · $651,596

## Abstract

ABSTRACT/SUMMARY
Development is an inherently dynamic process that operates on diverse timescales. Coordinating gene
expression, cell fate determination, and tissue growth is crucial in development, but our understanding is limited.
Through genetic analyses of C. elegans temporal patterning, we have discovered a molecular clock, composed
of circadian clock orthologs, that coordinates cell fate specification to developmental pace. It accomplishes this
task by generating oscillatory patterns of transcription that exhibit highly reproducible onset phases, durations,
and amplitudes. This clock regulates the transcriptional dosage of key microRNA (miRNA) genes that program
temporal cell fate transitions during development. The experiments outlined in this proposal aim to understand
the molecular underpinnings of this clock by determining the structures of three separate complexes
(protein::protein and protein::DNA) that assemble and disassemble in a specific order to tailor dynamic miRNA
transcriptional patterns. We will then use this knowledge to engineer clock component mutations that alter
features of these dynamic interactions. We will validate how these novel mutants affect complex assembly in
vitro and how they disturb development in vivo. Specifically, we hypothesize that these tailored mutations, both
loss-of- and gain-of-function, will alter miRNA transcriptional output by disrupting specific features of oscillatory
transcription (phase, amplitude, or duration). We will quantify changes in miRNA expression in these mutants by
directly monitoring miRNA transcriptional dynamics in mutant animals using a new state-of-the-art imaging
platform. This imaging system will also enable us to directly correlate changes in transcriptional dynamics to
alterations in temporal stem cell division patterns during development. In addition, we aim to use biochemical
strategies to identify the ligands that coordinate clock transcription factors. Identifying these ligands will reveal
how miRNA expression patterns sync across tissues to organize temporal patterning. Notably, many of the
physical interactions between the clock components we aim to study in the nematode system are conserved
between the mammalian orthologs. Therefore, these studies will not only shed light on how the timing of gene
expression contributes to developmental robustness but also may illuminate how transcription is coordinated
with metabolic changes during development.

## Key facts

- **NIH application ID:** 10973005
- **Project number:** 1R01GM155806-01
- **Recipient organization:** COLD SPRING HARBOR LABORATORY
- **Principal Investigator:** CHRISTOPHER Martin HAMMELL
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $651,596
- **Award type:** 1
- **Project period:** 2024-08-01 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10973005

## Citation

> US National Institutes of Health, RePORTER application 10973005, Molecular timekeeping and temporal cell fate specification in C. elegans (1R01GM155806-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10973005. Licensed CC0.

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