| Summary: | 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 (5mC) and 5-hydroxymethylcytosine (5hmC), with PacBio SingleMolecule Real-Time (SMRT) sequencing, we present here whole-genome long-read TAPS
(wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells
(mESCs) as a proof-of-concept, and an N50 read length of 3.5 kb is achieved. By sequencing
wglrTAPS to 8.2x depth, we discovered a significant proportion of CpG sites which were not covered
in previous 27.5x 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.
|
|---|