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Updated: Feb 20, 2026
Chromatin Isolation by RNA Purification ChIRP
Published on: March 25, 2012
Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA
Xueyin Wang1,2, Richard D Paucek1,2, Anne R Gooding1,2
1Department of Chemistry & Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
Abstract:
Many studies have revealed pathways of epigenetic gene silencing by Polycomb repressive complex 2 (PRC2) in vivo, but understanding the underlying molecular mechanisms requires biochemistry. Here we analyze interactions of reconstituted human PRC2 with nucleosome complexes. Histone modifications, the H3K27M cancer mutation, and inclusion of JARID2 or EZH1 in the PRC2 complex have unexpectedly minor effects on PRC2-nucleosome binding. Instead, protein-free linker DNA dominates the PRC2-nucleosome interaction. Specificity for CG-rich sequences is consistent with PRC2 occupying CG-rich DNA in vivo. PRC2 preferentially binds methylated DNA regulated by its AEBP2 subunit, suggesting how DNA and histone methylation collaborate to repress chromatin. We find that RNA, known to inhibit PRC2 activity, is not a methyltransferase inhibitor per se. Instead, RNA sequesters PRC2 from nucleosome substrates, because PRC2 binding requires linker DNA, and RNA and DNA binding are mutually exclusive. Together, we provide a model for PRC2 recruitment and an explanation for how actively transcribed genomic regions bind PRC2 but escape silencing.
Insights
Polycomb repressive complex 2 (PRC2) primarily binds to linker DNA, not histones, to silence genes. RNA inhibits PRC2 by competing for DNA binding, explaining gene silencing escape in active regions.
Area of Science:
- Biochemistry
- Molecular Biology
- Epigenetics
Background:
- Polycomb repressive complex 2 (PRC2) mediates epigenetic gene silencing in vivo.
- Understanding PRC2's molecular mechanisms necessitates biochemical investigation.
Purpose of the Study:
- To elucidate the molecular mechanisms of PRC2-nucleosome interactions.
- To investigate factors influencing PRC2 binding specificity and activity.
Main Methods:
- Biochemical analysis of reconstituted human PRC2 with nucleosome complexes.
- Assessing the impact of histone modifications, H3K27M mutation, and accessory proteins (JARID2, EZH1) on PRC2 binding.
- Investigating the role of DNA sequence, methylation, and RNA in PRC2 interactions.
Main Results:
- PRC2-nucleosome binding is dominated by interactions with protein-free linker DNA, not histone modifications or mutations.
- PRC2 exhibits specificity for CG-rich sequences and binds preferentially to methylated DNA via the AEBP2 subunit.
- RNA inhibits PRC2 by competing for DNA binding, rather than directly inhibiting methyltransferase activity.
Conclusions:
- PRC2 recruitment is primarily mediated by linker DNA, with CG-rich and methylated DNA enhancing binding.
- RNA-mediated sequestration of PRC2 from DNA explains how active genes can bind PRC2 without being silenced.
- This study provides a model for PRC2-mediated gene silencing and its regulation.
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