Beltran Manuel, Yates Christopher M, Skalska Lenka, Dawson Marcus, Reis Filipa P, Viiri Keijo, Fisher Cynthia L, Sibley Christopher R, Foster Benjamin M, Bartke Till, Ule Jernej, Jenner Richard G
UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom;
Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London WC1N 3BG, United Kingdom;
Genome Res. 2016 Jul;26(7):896-907. doi: 10.1101/gr.197632.115. Epub 2016 May 9.
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon-intron boundaries and the 3' UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.
多梳抑制复合物2（PRC2）修饰染色质，以便在发育过程中将基因维持在抑制状态。PRC2主要与抑制基因处的CpG岛相关联，并且还具有RNA结合活性。然而，在细胞中与PRC2结合的RNA、介导这些相互作用的亚基以及RNA在PRC2募集到染色质中的作用仍不清楚。通过对PRC2进行iCLIP并与其他RNA结合蛋白进行比较，我们在此表明PRC2在基本上所有活跃基因处结合新生RNA。尽管PRC2与RNA的相互作用较为广泛，但PRC2的结合在RNA内的特定位置富集，主要是外显子 - 内含子边界和3'UTR。缺失其他PRC2亚基表明，SUZ12足以建立这种RNA结合模式。与普遍模型相反，我们还证明，在细胞和体外，PRC2与RNA或染色质的相互作用是相互拮抗的。细胞中的RNA降解会触发PRC2募集到活跃基因处的CpG岛。相应地，细胞中PRC2从染色质上的释放会增加RNA结合。与此一致的是，在体外RNA和核小体竞争PRC2的结合。我们提出，RNA可阻止PRC2募集到活跃基因的染色质上，并且RNA与染色质之间的相互拮抗作用是PRC2在全基因组中染色质关联模式的基础。
