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Methodology for Accurate Detection of Mitochondrial DNA Methylation

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Published on: May 20, 2018

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.

Peng Ni^1,2,3, Fan Nie^1,2,3, Zeyu Zhong^1,3

¹School of Computer Science and Engineering, Central South University, Changsha, 410083, China.

Nature Communications

|July 8, 2023

Summary

We developed ccsmeth, a deep-learning tool for accurate DNA 5-methylcytosine (5mCpC) detection using PacBio circular consensus sequencing (CCS) reads. This method enhances methylation analysis in repetitive regions and offers haplotype-aware insights.

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Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Long-read sequencing technologies like PacBio CCS and nanopore sequencing show promise for detecting DNA 5-methylcytosine (5mCpG).
Existing PacBio CCS methods for 5mCpG detection lack accuracy and robustness, particularly in complex genomic regions.

Purpose of the Study:

To develop a novel deep-learning method, ccsmeth, for accurate and robust detection of DNA 5mCpGs using PacBio CCS reads.
To create a Nextflow pipeline, ccsmethphase, for haplotype-aware methylation detection from CCS data.

Main Methods:

Trained ccsmeth using PacBio CCS reads from polymerase-chain-reaction treated and M.SssI-methyltransferase treated human DNA.
Evaluated ccsmeth's performance on 5mCpG detection at single-molecule resolution using long CCS reads (≥10 Kb).
Developed ccsmethphase pipeline for haplotype-aware methylation analysis and validated it using a Chinese family trio.

Main Results:

ccsmeth achieved 0.90 accuracy and 0.97 Area Under the Curve for single-molecule 5mCpG detection.
Genome-wide site-level analysis showed >0.90 correlation with bisulfite and nanopore sequencing using only 10× CCS reads.
ccsmethphase successfully detected haplotype-aware methylation patterns.

Conclusions:

ccsmeth provides a robust and accurate deep-learning approach for DNA 5mCpG detection using PacBio CCS long reads.
ccsmethphase enables sensitive haplotype-aware methylation analysis, advancing epigenetic studies.
These tools offer significant improvements for DNA methylation analysis, especially in challenging genomic areas.