Selective identification of epigenetic regulators at methylated genomic sites by SelectID [ChIP-seq]
DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles in regulating gene expression and maintaining the repressive state of retrotransposon elements. However, accurate profiling of the proteomics which simultaneously identifies specific DNA sequences and their associated epigenetic modifications remains a challenge. Here, we report SelectID, which introduced methylated DNA binding domain into dCas9-mediated proximity labeling system to enable in situ protein capture at repetitive elements with 5-methylcytosine (5mC) modifications. SelectID were demonstrated as feasible as dCas9-TurboID system at specific DNA methylation regions, such as the chromosome 9 satellite. Using SelectID, we successfully identified CHD4 as potential repressors of methylated LINE-1 retrotransposon through direct binding at the 5'UTR of young LINE-1 elements. Overall, our SelectID approach has opened up new avenues for uncovering potential regulators of specific DNA regions with DNA methylation, which will greatly facilitate future studies on epigenetic regulation. Overall design: ChIP assays for dCas9 and MBD were conducted in Hela cells transfected with the SelectID cassettes targeting the Chr9 satellite region or L1 elements, using anti-MycTag and anti-Flag antibodies. CHD4 ChIP assays were performed in wild-type Hela cells using a CHD4 antibody. All experiments were carried out in duplicate.