qChIP-MS reveals the local chromatin composition by label-free quantitative proteomics.

Yong, Wai Khang; Zaal Anuar, Nurkaiyisah; Sin, Zi Wayne; Tan, Elayne Su Ru; Rane, Grishma; Shao, Xiaoman; Goh, Chai Yeen; Khanchandani, Vartika et al. · Nat Commun · 2026

basic_science · Level V

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Abstract

Chromatin immunoprecipitation (ChIP) has been a cornerstone for epigenetic analyses over the last decades, but even coupled to sequencing approaches (ChIP-seq), it is ultimately limited to one protein at a time. In a complementary effort, we here combine ChIP with label-free quantitative mass spectrometry (qChIP-MS) to interrogate local chromatin compositions. We demonstrate the versatility of our approach at telomeres, with transcription factors, in tissue and by dCas9-mediated locus-specific enrichment.