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

Author
item HARRIS, RICHARD - Baylor College Of Medicine
item WANG, TING - Washington University School Of Medicine
item COARFA, CHRISTIAN - Baylor College Of Medicine
item NAGARAJAN, RAMAN - University Of California
item HONG, CHIBO - University Of California
item DOWNEY, SARA - University Of California
item JOHNSON, BRETT - University Of California
item FOUSE, SHAUN - University Of California
item DELANEY, ALLEN - Genome Science Centre-Canada
item ZHAO, YONGJUN - Genome Science Centre-Canada
item OLSHEN, ADAM - University Of California
item BALLINGER, TRACY - University Of California
item ZHOU, XIN - Washington University School Of Medicine
item FORSBERG, KEVIN - Washington University School Of Medicine
item GU, JUNCHEN - Washington University School Of Medicine
item ECHIPARE, LORIGAIL - University Of California
item O'GEEN, HENRIETTE - University Of California
item LISTER, RYAN - Salk Institute Of Biological Studies
item PELIZZOLA, MATTIA - Salk Institute Of Biological Studies
item XI, YUANXIN - Baylor College Of Medicine
item EPSTEIN, CHARLES - Broad Institute Of Mit/harvard
item BERNSTEIN, BRADLEY - Ministry Of Science And Innovation, Csic
item HAWKINS, R.DAVID - University Of California
item REN, BING - University Of California
item CHUNG, WEN-YU - University Of Texas Southwestern Medical Center
item GU, HONGCANG - Broad Institute Of Mit/harvard
item BOCK, CHRISTOPH - Broad Institute Of Mit/harvard
item GNIRKE, ANDREAS - Broad Institute Of Mit/harvard
item ZHANG, MICHAEL - Cold Spring Harbor Laboratory
item HAUSSLER, DAVID - University Of California
item ECKER, JOSEPH - Salk Institute Of Biological Studies
item LI, WEI - Baylor College Of Medicine
item FARNHAM, PEGGY - University Of California
item Waterland, Robert - Children'S Nutrition Research Center (CNRC)
item ALEXANDER, MEISSNER - Broad Institute Of Mit/harvard
item MARRA, MARCO - Genome Science Centre-Canada
item HIRST, MARTIN - Genome Science Centre-Canada
item MILOSAVLJEVIC, ALEKSANDER - Baylor College Of Medicine
item COSTELLO, JOSEPH - University Of California

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2010
Publication Date: 9/19/2010
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.