iChIP ‐SILAC analysis identifies epigenetic regulators of CpG methylation of the p16INK4A gene

iChIP-SILAC identified DNMT1 and epigenetic regulators as proteins potentially interacting with a region of thep16INK4A gene that is CpG-methylated in one allele in HCT116 cells. Among the identified proteins, DDX24 contributed to the CpG methylation by regulating the protein level of DNMT1. iChIP is useful to identify proteins binding to a target locus. 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 thep16INK4A 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.

Source: FEBS Letters - April 17, 2024 Category: Biochemistry Authors: Toshitsugu Fujita, Hodaka Fujii Tags: Research Article Source Type: research