Open AccessIn vivo analysis of DNA methylation patterns recognized by specific proteins: coupling ChIP and bisulfite analysis
Author(s) -
Maria R. Matarazzo,
Francesca Lembo,
Tiziana Angrisano,
Esteban Ballestar,
Marcella Ferraro,
Raffaela Pero,
Maria Luigia De Bonis,
Carmelo B. Bruni,
Manel Esteller,
Maurizio D’Esposito,
Lorenzo Chiariotti
Publication year - 2004
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/04374dd02
Subject(s) - dna methylation , biology , methylation , epigenetics , epigenomics , chromatin , methylated dna immunoprecipitation , illumina methylation assay , chromatin immunoprecipitation , bisulfite sequencing , cpg site , chip sequencing , computational biology , epigenetics of physical exercise , genetics , chip on chip , dna , chromatin remodeling , gene , promoter , gene expression
The three-way connection between DNA methylation, chromatin configuration, and transcriptional regulation is under increasing attention, but the fine rules governing the epi-genetic control are still poorly understood. In several studies, the authors have concluded that the methylation status of CpG sites could be critical for the binding of factors to DNA and, consequently, for chromatin conformation. We tested the possibility that a novel technical approach combining chromatin immunoprecipitation and bisulfite genomic sequencing analysis (ChIP-BA) could provide useful information on the role of specific CpG methylation patterns in driving the association in vivo of proteins to given genomic regions. Our results show that ChIP-BA permits the establishment in vivo of the methylation patterns required for the binding of a methyl-CpG binding protein and, in addition, can potentially identify methylation patterns that do not allow a protein to bind specific genomic regions. Possible fields of application are discussed. We believe that wide use of ChIP-BA could make possible the exploration of a novel aspect of the intricate epigenetic web.