iChIP-SILAC analysis identifies epigenetic regulators of CpG methylation of the p16 INK4A gene.
Toshitsugu FujitaHodaka FujiiPublished in: FEBS letters (2024)
Allele-specific epigenetic events regulate the expression of specific genes such as tumor suppressor genes. Methods to biochemically identify epigenetic regulators remain limited. Here, we used insertional chromatin immunoprecipitation (iChIP) to address this issue. iChIP combined with quantitative mass spectrometry identified DNA methyltransferase 1 (DNMT1) and epigenetic regulators as proteins that potentially interact with a region of the p16 INK4A gene that is CpG-methylated in one allele in HCT116 cells. Some of the identified proteins are involved in the CpG methylation of this region, and of these, DEAD-box helicase 24 (DDX24) contributes to CpG methylation by regulating the protein levels of DNMT1. Thus, iChIP is a useful method to identify proteins which bind to a target locus of interest.
Keyphrases
- dna methylation
- genome wide
- gene expression
- copy number
- transcription factor
- mass spectrometry
- binding protein
- genome wide identification
- cell cycle arrest
- induced apoptosis
- poor prognosis
- high resolution
- liquid chromatography
- signaling pathway
- cell free
- oxidative stress
- single molecule
- gas chromatography
- high performance liquid chromatography
- data analysis
- tandem mass spectrometry
- amino acid
- bioinformatics analysis