Home LiteratureArticle Details
PMID: 18987807 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

The MIRA method for DNA methylation analysis.

Methods in molecular biology (Clifton, N.J.) ·Vol. 507 ·2009-00-00 ·Pages 65-75

Rauch TA, Pfeifer GP

Abstract

DNA methylation patterns are often altered in human cancer and aberrant methylation is considered a hallmark of malignant transformation. Several methods have been developed for the characterization of gene-specific and genome-wide DNA methylation patterns. In this chapter, we describe the methylated-CpG island recovery assay (MIRA), which is based on the high affinity of the MBD2b/MBD3L1 complex for double-stranded CpG-methylated DNA. MIRA has been used in combination with microarray platforms to map DNA methylation patterns across the human genome.

MeSH Terms
CpG Islands DNA/chemistry,isolation & purification DNA Methylation DNA-Binding Proteins Humans Oligonucleotide Array Sequence Analysis/methods Recombinant Fusion Proteins Repressor Proteins
Chemicals
DNA-Binding Proteins MBD2 protein MBD3L1 protein, human Recombinant Fusion Proteins Repressor Proteins DNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Rauch Tibor A
Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
Pfeifer Gerd P
References (24)
24 references, click to expand
  1. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.
    Nat Genet. 2000 Feb;24(2):132-8 PMID: 10655057
  2. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing.
    Cancer Res. 2007 Sep 15;67(18):8511-8 PMID: 17875690
  3. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer.
    Nat Genet. 2002 Jun;31(2):141-9 PMID: 11992124
  4. The fundamental role of epigenetic events in cancer.
    Nat Rev Genet. 2002 Jun;3(6):415-28 PMID: 12042769
  5. Pharmacologic unmasking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma.
    Cancer Cell. 2002 Dec;2(6):485-95 PMID: 12498717
  6. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.
    Nucleic Acids Res. 2003 Mar 15;31(6):1765-74 PMID: 12626718
  7. Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation.
    Cancer Res. 2003 May 1;63(9):2164-71 PMID: 12727835
  8. Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays.
    Cancer Res. 2003 Jul 1;63(13):3735-42 PMID: 12839967
  9. Chemical transformation of E. coli.
    Methods Mol Biol. 2003;235:49-53 PMID: 12904644
  10. CpG-rich islands and the function of DNA methylation.
    Nature. 1986 May 15-21;321(6067):209-13 PMID: 2423876
  11. Preparation of bacterial genomic DNA.
    Methods Mol Biol. 1995;46:141-7 PMID: 7550704
  12. Establishment of methylation-sensitive-representational difference analysis and isolation of hypo- and hypermethylated genomic fragments in mouse liver tumors.
    Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2284-9 PMID: 9122186
  13. Identification and characterization of a family of mammalian methyl-CpG binding proteins.
    Mol Cell Biol. 1998 Nov;18(11):6538-47 PMID: 9774669
  14. Epigenomic changes during leukemia cell differentiation: analysis of histone acetylation and cytosine methylation using CpG island microarrays.
    J Pharmacol Exp Ther. 2004 Dec;311(3):968-81 PMID: 15302897
  15. MBD3L1 is a transcriptional repressor that interacts with methyl-CpG-binding protein 2 (MBD2) and components of the NuRD complex.
    J Biol Chem. 2004 Dec 10;279(50):52456-64 PMID: 15456747
  16. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells.
    Nat Genet. 2005 Aug;37(8):853-62 PMID: 16007088
  17. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer.
    Lab Invest. 2005 Sep;85(9):1172-80 PMID: 16025148
  18. Profiling DNA methylation patterns using genomic tiling microarrays.
    Nat Methods. 2005 Mar;2(3):219-24 PMID: 16163803
  19. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH.
    Genes Chromosomes Cancer. 2005 Nov;44(3):305-19 PMID: 16075461
  20. Mutagenesis at methylated CpG sequences.
    Curr Top Microbiol Immunol. 2006;301:259-81 PMID: 16570852
  21. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells.
    Cancer Res. 2006 Aug 15;66(16):7939-47 PMID: 16912168
  22. Cancer epigenomics: DNA methylomes and histone-modification maps.
    Nat Rev Genet. 2007 Apr;8(4):286-98 PMID: 17339880
  23. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay.
    Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5527-32 PMID: 17369352
  24. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays.
    Cancer Res. 2001 Dec 1;61(23):8375-80 PMID: 11731411
Article Info
Journal
Methods in molecular biology (Clifton, N.J.)
Abbr.
Methods Mol Biol
ISSN
1064-3745
DOI
10.1007/978-1-59745-522-0_6
Published
2009-00-00
Pages
65-75
Language
English
Region
United States
NLM ID
9214969
PMCID
PMC2824570
Subset
IM
Grants
NCI NIH HHS · CA104967 · United States
NCI NIH HHS · R01 CA104967 · United States
NCI NIH HHS · R21 CA128495-02 · United States
NCI NIH HHS · R01 CA104967-05 · United States
NCI NIH HHS · CA128495 · United States
NCI NIH HHS · R21 CA128495 · United States
External Links
PubMed source DOI: 10.1007/978-1-59745-522-0_6 PMC Full Text
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2