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Selective identification of epigenetic regulators at methylated genomic sites by SelectID [RNA-seq]

GSE275612 Homo sapiens Expression profiling by high throughput sequencing 6 samples Submitted 2025/03/07 Platform GPL24676
Summary
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.
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Direct links to NCBI, no account and no request form: the whole study as GSE275612_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1152223 and SRA study SRP528508. Searching any of these in the dataset finder brings you back here.

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