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Updated: Jul 17, 2026
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Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples
Published on: August 29, 2017
A low-input CUT&RUN-qPCR method for histone modification profiling in Daphnia magna embryos
Nikko Adhitama1, Daffa Ramadhan Aridis2, Nong Dang Quang2
1Department of Biotechnology, Graduate School of Engineering, The University of Osaka, 2-1 Yamadaoka, Suita, Japan 565-0871; Institute for Open and Transdisciplinary Research Initiatives (OTRI), The University of Osaka, Suita, Japan 565-0871.
Gene
|July 15, 2026
Summary
We optimized a low-input CUT&RUN-qPCR method for Daphnia magna embryos to study epigenetic regulation of phenotypic plasticity. This technique successfully detected sex-biased histone modifications at the doublesex1 gene locus.
Area of Science:
- Ecology and Evolution
- Epigenetics
- Developmental Biology
Background:
- Phenotypic plasticity allows organisms to adapt to environmental changes.
- Histone modifications are key epigenetic regulators of phenotypic plasticity.
- Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is effective for profiling histone modifications.
Purpose of the Study:
- Adapt a low-input CUT&RUN-qPCR protocol for Daphnia magna embryos.
- Investigate histone modifications at the doublesex1 locus during sex determination.
- Establish a methodological basis for studying epigenetic underpinnings of phenotypic plasticity.
Main Methods:
- Developed a cell dissociation protocol for Daphnia embryos.
- Applied low-input CUT&RUN-qPCR to profile histone modifications.
- Utilized a dsx1 reporter strain for cell-specific analysis.
Main Results:
- Detected male-biased H3K4me3 enrichment at the dsx1 transcription start sites.
- Observed higher enrichment of repressive marks (H3K9me3, H3K27me3) in females.
- Demonstrated detection of sex-biased histone modifications from as few as 20 embryos.
Conclusions:
- CUT&RUN-qPCR is a practical method for histone modification profiling in Daphnia.
- Established a benchmark for CUT&RUN input requirements in low-input, heterogeneous samples.
- Provides a foundation for future research on epigenetics and phenotypic plasticity in Daphnia.
