Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

Abstract

Sequencing-based DNA methylation profiling methods are comprehensive and, as accuracy and affordability improve, will increasingly supplant microarrays for genome-scale analyses. Here, four sequencing-based methodologies were applied to biological replicates of human embryonic stem cells to compare their CpG coverage genome-wide and in transposons, resolution, cost, concordance and its relationship with CpG density and genomic context. The two bisulfite methods reached concordance of 82% for CpG methylation levels and 99% for non-CpG cytosine methylation levels. Using binary methylation calls, two enrichment methods were 99% concordant, while regions assessed by all four methods were 97% concordant. To achieve comprehensive methylome coverage while reducing cost, an approach integrating two complementary methods was examined. The integrative methylome profile along with histone methylation, RNA, and SNP profiles derived from the sequence reads allowed genome-wide assessment of allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.

Physiological regulation of transgene expression by a lentiviral vector containing the A2UCOE linked to a myeloid promoter

“…Nevertheless, these observations imply that A2UCOE simply supports the inherent epigenetic state and transcriptional activity of cellular promoters in P19 cells. This view is consistent with the fact that the MRP8 promoter in our vectors adopts the epigenetic state of its endogenous counterpart in ES cells (Supplementary Figure 3 and Harris et al 29 ; Hawkins et al 30 ; Wang et al 31 ). Accordingly, the A2UCOE chromatin remodeling activity does not interfere with the inherently encoded epigenetic state and transcriptional regulation of linked promoters, but prevents or reduces the influence of the chromosomal environment.…”

Surveying the epigenomic landscape, one base at a time

“…However, with the advent of massively parallel short-read DNA sequencing and its potential for single base-pair resolution, there has been a renaissance of interest in traditional methods for chromatin characterization, including the use of bisulfite sequencing for mapping DNA methylation [10] and the use of non-specific nucleases, including micrococcal nuclease (MNase) [11], deoxyribonuclease I (DNase I) [12] and exonuclease [13] (Table 1). Here, we focus on recently developed strategies for characterizing nucleosomes, TFs and chromatin-associated proteins at base-pair resolution, and we discuss prospects for full epigenome characterization.…”

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

“…Yet, these methods do neither provide single base pair (bp) resolution nor information regarding unmethylated alleles and are therefore not directly applicable to detect monoallelic events (20). While some approaches already tried to tackle this issue, they rely on the combination of multiple sequencing technologies, like, for example, the integrative method of Harris et al (21), which tries to find regions with intermediate and potentially monoallelic events by combining data originating from MeDIP-seq, methylation-sensitive restriction enzyme sequencing (MRE-seq), ribonucleic acid sequencing (RNAseq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq).…”