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

Release time:2025-03-05

DOI number:10.1038/s41467-023-39784-9

Journal:NATURE COMMUNICATIONS

Key Words:GENOME， BROWSER

Abstract:Existing methods for detecting DNA methylation (5mC) are less accurate and robust. Here, the authors develop a deep learning tool ccsmeth and a Nextflow pipeline ccsmethphase for genome-wide 5mCpG detection and phasing with high accuracy from CCS reads in human. Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (& GE;10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10x reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.

Note:Ni, P (Ni, Peng) [1] , [2] , [3] ; Nie, F (Nie, Fan) [1] , [2] , [3] ; Zhong, ZY (Zhong, Zeyu) [1] , [3] ; Xu, JR (Xu, Jinrui) [1] , [3] ; Huang, N (Huang, Neng) [1] , [3] ; Zhang, J (Zhang, Jun) [1] , [3] ; Zhao, HC (Zhao, Haochen) [1] , [3] ; Zou, Y (Zou, You) [1] , [3] ; Huang, YF (Huang, Yuanfeng) [4] ; Li, JC (Li, Jinchen) [4] , [5] ; Xiao, CL (Xiao, Chuan-Le) [6] ; Luo, F (Luo, Feng) [7] ; Wang, JX (Wang, Jianxin) [1] , [2] , [3]

Indexed by:Journal paper

Volume:14

Issue:1

Translation or Not:no

Date of Publication:2023-07-08

Included Journals:SCI