Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS

Genome Biol. 2020 Mar 3;21(1):54. doi: 10.1186/s13059-020-01969-6.

Abstract

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.

Keywords: 5-Methylcytosine; Bisulfite-free; DNA methylation; Epigenetic phasing; Long-read sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • 5-Methylcytosine / analysis
  • 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*

Substances

  • Boron Compounds
  • Proto-Oncogene Proteins
  • Pyridines
  • pyridine borane
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • DNA
  • Mixed Function Oxygenases
  • TET1 protein, human