Repository logo
 
Publication

Whole human genome 5’-mC methylation analysis using long read nanopore sequencing

2022-12Journal article Restricted access
Simple item page
dc.contributor.authorSilva, Catarina
dc.contributor.authorMachado, Miguel
dc.contributor.authorFerrão, José
dc.contributor.authorSebastião Rodrigues, António
dc.contributor.authorVieira, Luís
dc.date.accessioned2023-02-28T15:18:00Z
dc.date.available2023-02-28T15:18:00Z
dc.date.issued2022-12
dc.description.abstractMethylation microarray and bisulphite sequencing are often used to study 5'-methylcytosine (5'-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustworthy results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulphite and/or the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5'-mC since it allows sequencing of native DNA molecules, whereas the long reads produced by this technology help to increase the resolution of those genomic regions. In this work, we show that nanopore sequencing with 10X coverage depth, using DNA from a human cell line, produces 5'-mC methylation frequencies consistent with those obtained by 450k microarray, digital restriction enzyme analysis of methylation, and reduced representation bisulphite sequencing. High correlation between methylation frequencies obtained by nanopore sequencing and the other methodologies was also noticeable in either low or high GC content regions, including CpG islands and transcription start sites. We also showed that a minimum of five reads per CpG yields strong correlations (>0.89) in replicate nanopore sequencing runs and an almost uniform linearity of the methylation frequency variation between zero and one. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns based on genomic annotations of CpG regions. These results demonstrate that nanopore sequencing is a fast, robust, and reliable approach to the study of 5'-mC in the human genome with low coverage depth.pt_PT
dc.description.sponsorshipThis work is a result of the GenomePT project (POCI-01- 0145-FEDER-022184), supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT). This work was also supported by Fundos FEDER through the Programa Operacional Factores de Competitividade – COMPETE and by Fundos Nacionais through the FCT EPIGENETICS 1973 within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health-ToxOmics)pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationEpigenetics. 2022 Dec;17(13):1961-1975. doi: 10.1080/15592294.2022.2097473. Epub 2022 Jul 20.pt_PT
dc.identifier.doi10.1080/15592294.2022.2097473pt_PT
dc.identifier.issn1559-2294
dc.identifier.urihttp://hdl.handle.net/10400.18/8541
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherTaylor and Francis Grouppt_PT
dc.relationCentre for Toxicogenomics and Human Health
dc.relation.publisherversionhttps://www.tandfonline.com/doi/full/10.1080/15592294.2022.2097473pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subject5’-mC Methylationpt_PT
dc.subjectMinIONpt_PT
dc.subjectHuman Genomept_PT
dc.subjectMethylation-callingpt_PT
dc.subjectNanopore Sequencingpt_PT
dc.subjectDoenças Genéticaspt_PT
dc.subjectTecnologias de Análise de DNApt_PT
dc.titleWhole human genome 5’-mC methylation analysis using long read nanopore sequencingpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleCentre for Toxicogenomics and Human Health
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F00009%2F2019/PT
oaire.citation.endPage1975pt_PT
oaire.citation.issue13pt_PT
oaire.citation.startPage1961pt_PT
oaire.citation.titleEpigeneticspt_PT
oaire.citation.volume17pt_PT
oaire.fundingStream6817 - DCRRNI ID
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.embargofctAcesso de acordo com política editorial da revista.pt_PT
rcaap.rightsembargoedAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublicationda24f146-9eb6-459d-8a8d-8adef9929107
relation.isProjectOfPublication.latestForDiscoveryda24f146-9eb6-459d-8a8d-8adef9929107

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
Whole human genome 5 mC methylation analysis using long read nanopore sequencing.pdf
Size:
1.89 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

DDI - Artigos em revistas internacionais