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Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
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Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
Xue Yue1, Zhiyuan Xie1, Moran Li1
1Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
Nature Communications
|December 24, 2022
Summary
Researchers developed nanoHiMe-seq, a nanopore sequencing method to map histone modifications and DNA methylation on single DNA molecules. This technique reveals the intricate connections between these epigenetic marks across the genome.
Area of Science:
- Epigenetics
- Genomics
- Molecular Biology
Background:
- Histone modifications and DNA methylation are key epigenetic regulators.
- Understanding their interplay is crucial for cell function.
- Current methods struggle to analyze these marks genome-wide on single molecules.
Purpose of the Study:
- To develop a novel method for simultaneous genome-wide profiling of histone modifications and DNA methylation.
- To investigate the relationship between these epigenetic marks at a single-molecule level.
- To enable phased analysis of epigenetic patterns.
Main Methods:
- Developed nanoHiMe-seq, a nanopore sequencing technique.
- Utilized a methyltransferase for exogenous adenine labeling near modified nucleosomes.
- Employed a hidden Markov model for simultaneous detection of labeled adenines and CpG methylation.
- Implemented the nanoHiMe software package for data analysis.
Main Results:
- Demonstrated the utility, robustness, and sensitivity of nanoHiMe-seq.
- Successfully profiled DNA methylation and histone modifications at low sequencing depths.
- Enabled concurrent determination of phased DNA methylation and histone modification patterns.
- Probed the intrinsic connectivity between epigenetic marks genome-wide.
Conclusions:
- nanoHiMe-seq provides a powerful tool for single-molecule epigenomic analysis.
- The method facilitates a deeper understanding of the interplay between DNA methylation and histone modifications.
- This technique opens new avenues for studying epigenomic regulation in various biological contexts.
