A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-06-07

AUTHORS

Verity F Oliver, Jun Wan, Saurabh Agarwal, Donald J Zack, Jiang Qian, Shannath L Merbs

ABSTRACT

BACKGROUND: Growing evidence suggests that DNA methylation plays a role in tissue-specific differentiation. Current approaches to methylome analysis using enrichment with the methyl-binding domain protein (MBD) are restricted to large (≥1 μg) DNA samples, limiting the analysis of small tissue samples. Here we present a technique that enables characterization of genome-wide tissue-specific methylation patterns from nanogram quantities of DNA. RESULTS: We have developed a methodology utilizing MBD2b/MBD3L1 enrichment for methylated DNA, kinase pre-treated ligation-mediated PCR amplification (MeKL) and hybridization to the comprehensive high-throughput array for relative methylation (CHARM) customized tiling arrays, which we termed MeKL-chip. Kinase modification in combination with the addition of PEG has increased ligation-mediated PCR amplification over 20-fold, enabling >400-fold amplification of starting DNA. We have shown that MeKL-chip can be applied to as little as 20 ng of DNA, enabling comprehensive analysis of small DNA samples. Applying MeKL-chip to the mouse retina (a limited tissue source) and brain, 2,498 tissue-specific differentially methylated regions (T-DMRs) were characterized. The top five T-DMRs (Rgs20, Hes2, Nfic, Cckbr and Six3os1) were validated by pyrosequencing. CONCLUSIONS: MeKL-chip enables genome-wide methylation analysis of nanogram quantities of DNA with a wide range of observed-to-expected CpG ratios due to the binding properties of the MBD2b/MBD3L1 protein complex. This methodology enabled the first analysis of genome-wide methylation in the mouse retina, characterizing novel T-DMRs. More... »

PAGES

17-17

References to SciGraph publications

  • 2010-01-10. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution in NATURE METHODS
  • 2010-07. Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters in NATURE
  • 2011-09-21. The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity in NEURAL DEVELOPMENT
  • 2011-03-18. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling in NATURE PROTOCOLS
  • 2009-01-18. Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores in NATURE GENETICS
  • 2012-06-15. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood in GENOME BIOLOGY
  • 2005-07-18. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer in LABORATORY INVESTIGATION
  • 2011-05-11. Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development in BMC GENOMICS
  • 2010-09-19. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications in NATURE BIOTECHNOLOGY
  • 2010-09-19. Genome-wide mapping of DNA methylation: a quantitative technology comparison in NATURE BIOTECHNOLOGY
  • 2010-02-08. HELP (HpaII Tiny Fragment Enrichment by Ligation-Mediated PCR) Assay for DNA Methylation Profiling of Primary Normal and Malignant B Lymphocytes in MICROARRAY METHODS FOR DRUG DISCOVERY
  • 2012-03-08. Methylome analysis using MeDIP-seq with low DNA concentrations in NATURE PROTOCOLS
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    URI

    http://scigraph.springernature.com/pub.10.1186/1756-8935-6-17

    DOI

    http://dx.doi.org/10.1186/1756-8935-6-17

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23759032


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