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CUT&RUN for Chromatin Profiling in Caenorhabditis elegans
Felicity J Emerson1,2, Siu Sylvia Lee1
1Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York.
Current Protocols
|June 17, 2022
Summary
We developed a robust Cleavage under targets and release using nuclease (CUT&RUN) protocol for Caenorhabditis elegans. This method provides high-resolution chromatin profiles using minimal starting material, advancing genomic research in this model organism.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Cleavage under targets and release using nuclease (CUT&RUN) is a sensitive chromatin profiling technique.
- CUT&RUN offers high-resolution binding profiles with reduced sample input compared to ChIP.
- Its application in Caenorhabditis elegans has been limited due to technical challenges.
Purpose of the Study:
- To establish a robust CUT&RUN protocol for C. elegans.
- To enable high-resolution genome-wide mapping of protein factors and histone modifications in worms.
- To overcome cell dissociation challenges in C. elegans for chromatin profiling.
Main Methods:
- Developed a simple, live-tissue CUT&RUN protocol for C. elegans.
- Optimized worm dissociation for uniform permeabilization without cell damage.
- Detailed protocols for worm growth, sample prep, CUT&RUN workflow, library prep, and data analysis.
Main Results:
- Achieved high-quality CUT&RUN profiles from as few as 100 worms.
- Demonstrated detectable signal with as few as 10 worms.
- Protocol is accessible for routine use in worm labs.
Conclusions:
- The developed CUT&RUN protocol is effective and sensitive for C. elegans.
- This method significantly reduces the required starting material compared to ChIP.
- Enables physiologically relevant, high-resolution chromatin profiling in C. elegans.
