Literature DB >> 18987807

The MIRA method for DNA methylation analysis.

Tibor A Rauch1, Gerd P Pfeifer.   

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.

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Year:  2009        PMID： 18987807      PMCID： PMC2824570          DOI： 10.1007/978-1-59745-522-0_6

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  24 in total

1.  A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer.

Authors:  Hiromu Suzuki; Edward Gabrielson; Wei Chen; Ramaswamy Anbazhagan; Manon van Engeland; Matty P Weijenberg; James G Herman; Stephen B Baylin
Journal:  Nat Genet       Date:  2002-05-06       Impact factor: 38.330

2.  Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.

Authors:  J F Costello; M C Frühwald; D J Smiraglia; L J Rush; G P Robertson; X Gao; F A Wright; J D Feramisco; P Peltomäki; J C Lang; D E Schuller; L Yu; C D Bloomfield; M A Caligiuri; A Yates; R Nishikawa; H Su Huang; N J Petrelli; X Zhang; M S O'Dorisio; W A Held; W K Cavenee; C Plass
Journal:  Nat Genet       Date:  2000-02       Impact factor: 38.330

3.  Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation.

Authors:  Huidong Shi; Susan H Wei; Yu-Wei Leu; Farahnaz Rahmatpanah; Joseph C Liu; Pearlly S Yan; Kenneth P Nephew; Tim Hui-Ming Huang
Journal:  Cancer Res       Date:  2003-05-01       Impact factor: 12.701

4.  Chemical transformation of E. coli.

Authors:  W Edward Swords
Journal:  Methods Mol Biol       Date:  2003

Review 5.  CpG-rich islands and the function of DNA methylation.

Authors:  A P Bird
Journal:  Nature       Date:  1986 May 15-21       Impact factor: 49.962

6.  The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.

Authors:  Mario F Fraga; Esteban Ballestar; Guillermo Montoya; Panya Taysavang; Paul A Wade; Manel Esteller
Journal:  Nucleic Acids Res       Date:  2003-03-15       Impact factor: 16.971

Review 7.  The fundamental role of epigenetic events in cancer.

Authors:  Peter A Jones; Stephen B Baylin
Journal:  Nat Rev Genet       Date:  2002-06       Impact factor: 53.242

8.  Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing.

Authors:  Kristen H Taylor; Robin S Kramer; J Wade Davis; Juyuan Guo; Deiter J Duff; Dong Xu; Charles W Caldwell; Huidong Shi
Journal:  Cancer Res       Date:  2007-09-15       Impact factor: 12.701

9.  Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays.

Authors:  Norihiro Sato; Noriyoshi Fukushima; Anirban Maitra; Hiroyuki Matsubayashi; Charles J Yeo; John L Cameron; Ralph H Hruban; Michael Goggins
Journal:  Cancer Res       Date:  2003-07-01       Impact factor: 12.701

10.  Pharmacologic unmasking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma.

Authors:  Keishi Yamashita; Sunil Upadhyay; Motonobu Osada; Mohammad O Hoque; Yan Xiao; Masaki Mori; Fumiaki Sato; Stephen J Meltzer; David Sidransky
Journal:  Cancer Cell       Date:  2002-12       Impact factor: 31.743
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  25 in total

Review 1.  Using DNA methylation to understand biological consequences of genetic variability.

Authors:  Dena G Hernandez; Andrew B Singleton
Journal:  Neurodegener Dis       Date:  2011-11-26       Impact factor: 2.977

Review 2.  Human non-CG methylation: are human stem cells plant-like?

Authors:  Olga V Dyachenko; Tara V Schevchuk; Leo Kretzner; Yaroslav I Buryanov; Steven S Smith
Journal:  Epigenetics       Date:  2010-10-01       Impact factor: 4.528

Review 3.  Advances in epigenetics and epigenomics for neurodegenerative diseases.

Authors:  Irfan A Qureshi; Mark F Mehler
Journal:  Curr Neurol Neurosci Rep       Date:  2011-10       Impact factor: 5.081

Review 4.  Principles and challenges of genomewide DNA methylation analysis.

Authors:  Peter W Laird
Journal:  Nat Rev Genet       Date:  2010-03       Impact factor: 53.242

Review 5.  Epigenetic mechanisms in diabetic vascular complications.

Authors:  Marpadga A Reddy; Rama Natarajan
Journal:  Cardiovasc Res       Date:  2011-01-25       Impact factor: 10.787

6.  Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

Authors:  Jung H Kim; Saravana M Dhanasekaran; John R Prensner; Xuhong Cao; Daniel Robinson; Shanker Kalyana-Sundaram; Christina Huang; Sunita Shankar; Xiaojun Jing; Matthew Iyer; Ming Hu; Lee Sam; Catherine Grasso; Christopher A Maher; Nallasivam Palanisamy; Rohit Mehra; Hal D Kominsky; Javed Siddiqui; Jindan Yu; Zhaohui S Qin; Arul M Chinnaiyan
Journal:  Genome Res       Date:  2011-07       Impact factor: 9.043

7.  CpG island hypermethylation in human astrocytomas.

Authors:  Xiwei Wu; Tibor A Rauch; Xueyan Zhong; William P Bennett; Farida Latif; Dietmar Krex; Gerd P Pfeifer
Journal:  Cancer Res       Date:  2010-03-16       Impact factor: 12.701

8.  The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells.

Authors:  S Kalari; M Jung; K H Kernstine; T Takahashi; G P Pfeifer
Journal:  Oncogene       Date:  2012-08-20       Impact factor: 9.867

9.  DNA hypermethylation accompanied by transcriptional repression in follicular lymphoma.

Authors:  Lynda B Bennett; Jennifer L Schnabel; Jean M Kelchen; Kristen H Taylor; Juyuan Guo; Gerald L Arthur; Christos N Papageorgio; Huidong Shi; Charles W Caldwell
Journal:  Genes Chromosomes Cancer       Date:  2009-09       Impact factor: 5.006

10.  MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

Authors:  David Serre; Byron H Lee; Angela H Ting
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971
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