title: MIRA-seq for DNA methylation analysis of CpG islands.
abstract: OBJECTIVE
  To develop a reliable method for whole genome analysis of DNA methylation.
  
  
  METHODS
  Genome-scale analysis of DNA methylation includes affinity-based approaches such as enrichment using methyl-CpG-binding proteins. One of these methods, the methylated-CpG island recovery assay (MIRA), is based on the high affinity of the MBD2b-MBD3L1 complex for CpG-methylated DNA. Here we provide a detailed description of MIRA and combine it with next generation sequencing platforms (MIRA-seq).
  
  
  RESULTS
  We assessed the performance of MIRA-seq and compared the data with whole genome bisulfite sequencing.
  
  
  CONCLUSIONS
  MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions. The method is not limited by primer or probe design and is cost effective.
authors.affiliation: Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Jung
authors.affiliation: Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
authors.forename: Swati
authors.initials: S
authors.lastname: Kadam
authors.affiliation: Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
authors.forename: Wenying
authors.initials: W
authors.lastname: Xiong
authors.affiliation: Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA.
authors.forename: Tibor A
authors.initials: TA
authors.lastname: Rauch
authors.affiliation: Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.|Van Andel Research Institute, Grand Rapids, MI 49503, USA.
authors.forename: Seung-Gi
authors.initials: SG
authors.lastname: Jin
authors.affiliation: Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.|Van Andel Research Institute, Grand Rapids, MI 49503, USA.
authors.forename: Gerd P
authors.initials: GP
authors.lastname: Pfeifer
mesh_terms: D002460:Cell Line; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D015894:Genome, Human / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D015203:Reproducibility of Results
keywords: CpG islands; DNA methylation; high-throughput sequencing; methyl-CpG-binding protein; methylated-CpG island recovery assay