In vivo analysis of DNA methylation patterns recognized by specific proteins: coupling CHIP and bisulfite analysis.
The three-way connection between DNA methylation, chromatin configuration, and transcriptional regulation is under increasing attention, but the fine rules governing the epigenetic 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.
Matarazzo
Maria Rosaria
MR
Institute of Genetics and Biophysics, C.N.R., Naples, Italy.
Lembo
Francesca
F
Angrisano
Tiziana
T
Ballestar
Esteban
E
Ferraro
Marcella
M
Pero
Raffaela
R
De Bonis
Maria Luigia
ML
Bruni
Carmelo Bruno
CB
Esteller
Manel
M
D'Esposito
Maurizio
M
Chiariotti
Lorenzo
L
D001483:Base Sequence; D047369:Chromatin Immunoprecipitation / Q000295:instrumentation / Q000379:methods*; D003001:Cloning, Molecular; D003470:Culture Media; D004247:DNA / Q000378:metabolism*; D016172:DNA Fingerprinting; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D023281:Genomics; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D013431:Sulfates / Q000737:chemistry*
D003470:Culture Media; D004268:DNA-Binding Proteins; D013431:Sulfates; C012036:sodium sulfate; D004247:DNA