ARS | Publication request: Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2010
Publication Date: September 19, 2010
Citation: Harris, R.A., Wang, T., Coarfa, C., Nagarajan, R.P., Hong, C., Downey, S.L., Johnson, B.E., Fouse, S.D., Delaney, A., Zhao, Y., Olshen, A., Ballinger, T., Zhou, X., Forsberg, K.J., Gu, J., Echipare, L., O'Geen, H., Lister, R., Pelizzola, M., Xi, Y., Epstein, C.B., Bernstein, B.E., Hawkins, R., Ren, B., Chung, W., Gu, H., Bock, C., Gnirke, A., Zhang, M.Q., Haussler, D., Ecker, J.R., Li, W., Farnham, P.J., Waterland, R., Alexander, M., Marra, M.A., Hirst, M., Milosavljevic, A., Costello, J.F. 2010. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28:1097-1105.

Interpretive Summary: Epigenetic mechanisms are gene regulatory mechanisms that are layered on top of the DNA sequence information and, like DNA sequence, are copied and maintained as cells in the body divide and replenish themselves throughout life. Just as the human genome project sequenced the entire human genome, yielding insights into human disease, efforts are now underway to characterize epigenetic marks across the entire human genome. This is referred to as the human epigenome project. Whereas each person has just one genome (his/her entire genetic sequence) each person has hundreds or perhaps even thousands of diverse epigenomes, corresponding to different cell types and potential variation at the cell-specific level. Hence, the human epigenome project is a daunting task. A key epigenetic mark is DNA methylation, the addition of methyl groups (CH3) to cytosine, one of the four bases that comprise the sequence of DNA. This paper describes the comparison of different methods to measure DNA methylation across the human genome. It supports the validity of new sequencing-based methods that enable DNA methylation across the entire human genome to be characterized faster and cheaper than ever before possible. These methods will be applied in the human epigenome project.

Technical Abstract: Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.