Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- Michael Stevens1,
- Jeffrey B Cheng2,
- Daofeng Li1,
- Mingchao Xie1,
- Chibo Hong2,
- Cécile L Maire3,
- Keith L Ligon3,
- Martin Hirst4,
- Marco A Marra4,
- Joseph F Costello2 and
- Ting Wang5,6
- 1 Washington University;
- 2 UCSF;
- 3 Dana-Farber Cancer Institute;
- 4 Canada's Michael Smith Genome Sciences Centre;
- 5 Washington University School of Medicine
- ↵* Corresponding author; email: twang{at}genetics.wustl.edu
Abstract
Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole genome bisulfite sequencing (WGBS, MethylC-seq or BS-seq), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq and MRE-seq. These methods yield largely comparable results, but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel Conditional Random Fields-based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole genome bisulfite sequencing methods. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing and locus specific-bisulfite sequencing performed on the same embryonic stem cell line. MethylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage and resolution. We used conventional bisulfite conversion, PCR, cloning and sequencing to validate loci where our predictions do not agree with whole genome bisulfite data, and in 11 out of 12 cases methylCRF predictions of methylation level agree better with validated results than does whole genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive and widely accessible strategy to create full DNA methylomes.
- Received November 18, 2012.
- Accepted June 13, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
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