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NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine
Daoshan Zheng1, Justyna Trynda1, Zhifu Sun2
1Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA.
BMC Genomics
|July 4, 2019
Summary
NUCLIZE provides single-nucleosome resolution for histone modifications, revealing specific epigenetic patterns near transcription start sites. This quantitative epigenomic data enables deeper functional epigenomics studies.
Area of Science:
- Epigenetics
- Genomics
- Molecular Biology
Background:
- Current histone modification databases (e.g., ENCODE, Roadmap) lack single-nucleosome resolution due to ChIP-Seq limitations.
- Low-resolution data (several kilobase pairs) hinders accurate epigenomic information at the individual nucleosome level.
Purpose of the Study:
- To develop a method for generating histone modification data at single-nucleosome resolution.
- To enable quantitative epigenomic analysis of individual nucleosomes.
Main Methods:
- Developed NUCLIZE, a novel approach combining ChIP-Seq and high-resolution native MNase-Seq data.
- Synergistically analyzed histone modification and nucleosome mapping data.
Main Results:
- Generated quantitative epigenomics data for single and multivalent histone modifications per nucleosome.
- Identified defined, specific patterns of dominant trivalent histone marks (H3K4me3/H3K9ac/H3K27ac) near transcription start sites (TSS).
- These patterns suggest potential epigenetic codes regulating gene transcription.
Conclusions:
- Single-nucleosome resolution transforms epigenomic data into a quantitative format.
- This is crucial for studying dynamic epigenetic regulation and functional epigenomics.
- NUCLIZE facilitates the transition from epigenomic mapping to genuine functional epigenomics studies.
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