Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS.
5-Methylcytosine
/ analogs & derivatives
Animals
Boron Compounds
/ chemistry
Cells, Cultured
DNA
/ chemistry
DNA Methylation
Hep G2 Cells
Humans
Mice
Mixed Function Oxygenases
/ metabolism
Nanopore Sequencing
/ methods
Oxidation-Reduction
Proto-Oncogene Proteins
/ metabolism
Pyridines
/ chemistry
Sequence Analysis, DNA
/ methods
5-Methylcytosine
Bisulfite-free
DNA methylation
Epigenetic phasing
Long-read sequencing
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
03 03 2020
03 03 2020
Historique:
received:
03
12
2019
accepted:
21
02
2020
entrez:
5
3
2020
pubmed:
5
3
2020
medline:
5
1
2021
Statut:
epublish
Résumé
We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compatible with both Oxford Nanopore and PacBio Single-Molecule Real-Time (SMRT) sequencing, lrTAPS detects methylation with accuracy comparable to short-read Illumina sequencing but with long-range epigenetic phasing. We applied lrTAPS to sequence difficult-to-map regions in mouse embryonic stem cells and to identify distinct methylation events in the integrated hepatitis B virus genome.
Identifiants
pubmed: 32127008
doi: 10.1186/s13059-020-01969-6
pii: 10.1186/s13059-020-01969-6
pmc: PMC7053107
doi:
Substances chimiques
Boron Compounds
0
Proto-Oncogene Proteins
0
Pyridines
0
pyridine borane
110-51-0
5-hydroxymethylcytosine
1123-95-1
5-Methylcytosine
6R795CQT4H
DNA
9007-49-2
Mixed Function Oxygenases
EC 1.-
TET1 protein, human
EC 1.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
54Subventions
Organisme : Cancer Research UK
ID : C63763/A26394
Pays : United Kingdom
Organisme : Department of Health
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 200838/Z/16/Z
Pays : United Kingdom
Organisme : Medical Research Council (GB)
ID : MR/R022011/1
Pays : International
Organisme : Medical Research Council
ID : G0801976
Pays : United Kingdom
Organisme : Wellcome Trust
ID : IA 200838/Z/16/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : G0400802
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C63763/A27122
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R022011/1
Pays : United Kingdom
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