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Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation

Hall Hickman, Alexander; Jenner, Richard G; (2024) Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation. Cell Reports , 43 (3) , Article 113856. 10.1016/j.celrep.2024.113856. Green open access

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Abstract

Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages. In vitro, RNA inhibits PRC2 activity, but the effect of RNA on PRC2 in cells is less clear, with studies concluding that RNA either antagonizes or promotes PRC2 chromatin association. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of RNA bridges connecting PRC2 to chromatin. Here, we show that the apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation precipitates chromatin out of solution, thereby masking enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid rescues detection of PRC2 chromatin occupancy upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells.

Type: Article
Title: Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.celrep.2024.113856
Publisher version: http://dx.doi.org/10.1016/j.celrep.2024.113856
Language: English
Additional information: © 2024 The Authors. Published by Elsevier under a Creative Commons license (http://creativecommons.org/licenses/by/4.0/).
Keywords: RNA, non-coding RNA, chromatin, epigenetics, polycomb repressive complex 2, H3K27me3, RNase A, ChIP-seq, rChIP
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/10188395
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