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      Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

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          Abstract

          Aim:

          DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods.

          Material & methods:

          Following the success of the HumanMethylation450 BeadChip (Infinium) methylation microarray (450K), we report the technical and biological validation of the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the 450K sites, but adds 333,265 CpGs located in enhancer regions identified by the ENCODE and FANTOM5 projects.

          Results & conclusion:

          The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embeded samples and is also useful for 5-hydroxymethylcytosine. These results highlight the value of the MethylationEPIC BeadChip as a useful tool for the analysis of the DNA methylation profile of the human genome.

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          Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome.

          Marina Bibikova, Sebastian Moran, Juan Sandoval … (2011)
          DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases. Since cancer has highlighted the contribution to disease of aberrant DNA methylation patterns, such as the presence of promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and global DNA hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances in obtaining comprehensive DNA methylomes are hampered by the high cost and time-consuming aspects of the single nucleotide methods currently available for whole genome DNA methylation analyses. Following the success of the standard CpG methylation microarrays for 1,505 CpG sites and 27,000 CpG sites, we have validated in vivo the newly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500 bp, 5'-UTRs and exons 1) for coding genes, but also for the corresponding gene bodies and 3'-UTRs, in addition to intergenic regions derived from GWAS studies. Herein, we demonstrate that the 450K DNA methylation array can consistently and significantly detect CpG methylation changes in the HCT-116 colorectal cancer cell line in comparison with normal colon mucosa or HCT-116 cells with defective DNA methyltransferases (DKO). The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects.
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            Gateways to the FANTOM5 promoter level mammalian expression atlas

            Marina Lizio, Jayson Harshbarger, Hisashi Shimoji … (2015)
            The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users.
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              Enhancers: five essential questions.

              Len Pennacchio, Wendy Bickmore, Ann Dean … (2013)
              It is estimated that the human genome contains hundreds of thousands of enhancers, so understanding these gene-regulatory elements is a crucial goal. Several fundamental questions need to be addressed about enhancers, such as how do we identify them all, how do they work, and how do they contribute to disease and evolution? Five prominent researchers in this field look at how much we know already and what needs to be done to answer these questions.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Epigenomics
                Journal ID (iso-abbrev): Epigenomics
                Journal ID (publisher-id): EPI
                Title: Epigenomics
                Publisher: Future Medicine Ltd (London, UK )
                ISSN (Print): 1750-1911
                ISSN (Electronic): 1750-192X
                Publication date (Print): March 2016
                Publication date (Electronic): 17 December 2015
                Volume: 8
                Issue: 3
                Pages: 389-399
                Affiliations
                [1 ]Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain
                [2 ]Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
                [3 ]Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
                Author notes
                *Author for correspondence: mesteller@ 123456idibell.cat
                Article
                DOI: 10.2217/epi.15.114
                PMC ID: 4864062
                PubMed ID: 26673039
                SO-VID: 5770478a-90e5-4e32-8a52-cfa6331e6757
                Copyright © © M Esteller
                License:

                This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 Unported License

                History
                Date received : 18 November 2015
                Date accepted : 02 December 2015
                Categories
                Subject: Special Report

                Keywords: 5-hydroxymethylcytosine,cpg sites,dna methylation,epigenetics,microarray,paraffin,validation
                Data availability:
                Keywords: 5-hydroxymethylcytosine, cpg sites, dna methylation, epigenetics, microarray, paraffin, validation

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