Whole-genome Long-read TAPS Deciphers DNA Methylation Patterns at Base Resolution Using PacBio SMRT Sequencing Technology

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2022 Jul 18

PMID 35849350

Authors

Jinfeng Chen

Jingfei Cheng

Xiufei Chen

Masato Inoue

Yibin Liu

Chun-Xiao Song

Affiliations

Soon will be listed here.

Abstract

Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.

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References

Jin Z, Liu Y . DNA methylation in human diseases. Genes Dis. 2018; 5(1):1-8. PMC: 6147084. DOI: 10.1016/j.gendis.2018.01.002. View

Sun Z, Vaisvila R, Hussong L, Yan B, Baum C, Saleh L . Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res. 2021; 31(2):291-300. PMC: 7849414. DOI: 10.1101/gr.265306.120. View

Hanna C, Kelsey G . Genomic imprinting beyond DNA methylation: a role for maternal histones. Genome Biol. 2017; 18(1):177. PMC: 5605981. DOI: 10.1186/s13059-017-1317-9. View

Lappalainen T, Scott A, Brandt M, Hall I . Genomic Analysis in the Age of Human Genome Sequencing. Cell. 2019; 177(1):70-84. PMC: 6532068. DOI: 10.1016/j.cell.2019.02.032. View

Sakamoto Y, Zaha S, Nagasawa S, Miyake S, Kojima Y, Suzuki A . Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing. Nucleic Acids Res. 2021; 49(14):e81. PMC: 8373077. DOI: 10.1093/nar/gkab397. View

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M . Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2015; 32(8):1220-2. DOI: 10.1093/bioinformatics/btv710. View

Wenger A, Peluso P, Rowell W, Chang P, Hall R, Concepcion G . Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019; 37(10):1155-1162. PMC: 6776680. DOI: 10.1038/s41587-019-0217-9. View

Dammann R, Kirsch S, Schagdarsurengin U, Dansranjavin T, Gradhand E, Schmitt W . Frequent aberrant methylation of the imprinted IGF2/H19 locus and LINE1 hypomethylation in ovarian carcinoma. Int J Oncol. 2009; 36(1):171-9. View

Olivia Tse O, Jiang P, Cheng S, Peng W, Shang H, Wong J . Genome-wide detection of cytosine methylation by single molecule real-time sequencing. Proc Natl Acad Sci U S A. 2021; 118(5). PMC: 7865158. DOI: 10.1073/pnas.2019768118. View

10.

Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z . Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 2020; 21(1):189. PMC: 7477834. DOI: 10.1186/s13059-020-02107-y. View

11.

Chaisson M, Sanders A, Zhao X, Malhotra A, Porubsky D, Rausch T . Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019; 10(1):1784. PMC: 6467913. DOI: 10.1038/s41467-018-08148-z. View

12.

Esteller M . Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet. 2007; 8(4):286-98. DOI: 10.1038/nrg2005. View

13.

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

14.

Delaneau O, Howie B, Cox A, Zagury J, Marchini J . Haplotype estimation using sequencing reads. Am J Hum Genet. 2013; 93(4):687-96. PMC: 3791270. DOI: 10.1016/j.ajhg.2013.09.002. View

15.

Tanaka K, Okamoto A . Degradation of DNA by bisulfite treatment. Bioorg Med Chem Lett. 2007; 17(7):1912-5. DOI: 10.1016/j.bmcl.2007.01.040. View

16.

Robertson K . DNA methylation and human disease. Nat Rev Genet. 2005; 6(8):597-610. DOI: 10.1038/nrg1655. View

17.

Logsdon G, Vollger M, Eichler E . Long-read human genome sequencing and its applications. Nat Rev Genet. 2020; 21(10):597-614. PMC: 7877196. DOI: 10.1038/s41576-020-0236-x. View

18.

Qi W, Lim Y, Patrignani A, Schlapfer P, Bratus-Neuenschwander A, Gruter S . The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. Gigascience. 2022; 11. PMC: 8952263. DOI: 10.1093/gigascience/giac028. View

19.

De Coster W, De Rijk P, De Roeck A, De Pooter T, DHert S, Strazisar M . Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. Genome Res. 2019; 29(7):1178-1187. PMC: 6633254. DOI: 10.1101/gr.244939.118. View

20.

Zhao L, Song J, Liu Y, Song C, Yi C . Mapping the epigenetic modifications of DNA and RNA. Protein Cell. 2020; 11(11):792-808. PMC: 7647981. DOI: 10.1007/s13238-020-00733-7. View