Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer.
Methyl-CpG binding proteins (MBDs) mediate histone deacetylase-dependent transcriptional silencing at methylated CpG islands. Using chromatin immunoprecitation (ChIP) we have found that gene-specific profiles of MBDs exist for hypermethylated promoters of breast cancer cells, whilst a common pattern of histone modifications is shared. This unique distribution of MBDs is also characterized in chromosomes by comparative genomic hybridization of immunoprecipitated DNA and immunolocalization. Most importantly, we demonstrate that MBD association to methylated DNA serves to identify novel targets of epigenetic inactivation in human cancer. We combined the ChIP assay of MBDs with a CpG island microarray (ChIP on chip). The scenario revealed shows that, while many genes are regulated by multiple MBDs, others are associated with a single MBD. These target genes displayed methylation- associated transcriptional silencing in breast cancer cells and primary tumours. The candidates include the homeobox gene PAX6, the prolactin hormone receptor, and dipeptidylpeptidase IV among others. Our results support an essential role for MBDs in gene silencing and, when combined with genomic strategies, their potential to 'catch' new hypermethylated genes in cancer.
Ballestar
Esteban
E
Epigenetics Laboratory, Molecular Pathology Programme, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
Paz
Maria F
MF
Valle
Laura
L
Wei
Susan
S
Fraga
Mario F
MF
Espada
Jesus
J
Cigudosa
Juan Cruz
JC
Huang
Tim Hui-Ming
TH
Esteller
Manel
M
D044503:5-Methylcytosine / Q000032:analysis; D000595:Amino Acid Sequence; D001943:Breast Neoplasms; D002843:Chromatin / Q000235:genetics / Q000648:ultrastructure; D002868:Chromosomal Proteins, Non-Histone; D002874:Chromosome Mapping; D018899:CpG Islands / Q000502:physiology; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005260:Female; D006801:Humans; D051783:Methyl-CpG-Binding Protein 2; D018613:Microscopy, Confocal; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010446:Peptide Fragments / Q000737:chemistry; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism; D014407:Tumor Cells, Cultured
D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; C115369:MBD3 protein, human; C497392:MECP2 protein, human; D051783:Methyl-CpG-Binding Protein 2; D010446:Peptide Fragments; D012097:Repressor Proteins; D044503:5-Methylcytosine