The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion

• DOI: 10.1016/j.celrep.2024.113858
• Publication Date: 2024-02-27T17:42:04Z
• Authors: Evan Healy; Qi Zhang; Emma H. Gail; Samuel C. Agius; Guizhi Sun; Michael Bullen; Varun Pandey; Partha Pratim Das; Jose M. Polo; Chen Davidovich
• Keywords: PRC2; Occupancy; Artifact (error)

RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence favor against this idea. RNase treatment is commonly used to study RNA-mediated regulation but limitations approach remain unclear. A during immunoprecipitation (ChIP) reduces occupancy H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led suggestions an "RNA bridge" between PRC2 chromatin. Here, we show that ChIP causes apparent loss all facultative heterochromatin, including both genome-wide. We track observation a gain DNA from non-targeted chromatin, sequenced at expense which signals. Our results emphasize substantial using for mapping RNA-dependent invalidate conclusions were previously established based on assay.