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Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing
Jinfeng Chen1,2, Jingfei Cheng1,2, Xiufei Chen1,2
1Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
Nucleic Acids Research
|July 18, 2022
Summary
Whole-genome long-read TAPS (wglrTAPS) directly detects DNA methylation across entire genomes. This method improves mapping in difficult genomic regions, complementing short-read sequencing for epigenetics research.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- Long-read sequencing offers insights into complex genomic regions.
- Accurate, long-distance DNA methylation detection at a whole-genome scale is limited.
- Existing methods struggle with repetitive elements and structural variations.
Purpose of the Study:
- To develop a whole-genome long-read sequencing method for DNA methylation detection.
- To combine TET-assisted pyridine borane sequencing (TAPS) with PacBio single-molecule real-time sequencing.
- To enhance the resolution of DNA methylation patterns in challenging genomic areas.
Main Methods:
- Developed whole-genome long-read TAPS (wglrTAPS) by integrating TAPS with PacBio SMRT sequencing.
- Applied wglrTAPS to mouse embryonic stem cells for performance evaluation.
- Sequenced samples to achieve a 3.5 kb N50 read length and 8.2× depth.
Main Results:
- wglrTAPS successfully profiled DNA methylation across the mouse genome.
- Identified a significant number of CpG sites missed by previous short-read TAPS.
- Demonstrated improved methylation profiling in repetitive elements and structural variations.
- Enabled allelic methylation analysis, which is difficult for short-read methods.
Conclusions:
- wglrTAPS enhances DNA epigenetics applications using third-generation sequencing.
- The method overcomes limitations of short-read sequencing for methylation analysis in complex genomic regions.
- wglrTAPS provides a powerful tool for comprehensive, long-range epigenetic studies.
