Structural basis for inactivation of PRC2 by G-quadruplex RNA

Abstract

The histone methyltransferase PRC2 (Polycomb Repressive Complex 2) silences genes via successively attaching three methyl groups to lysine 27 of histone H3. PRC2 associates with numerous pre-mRNA and lncRNA transcripts with a binding preference for G-quadruplex RNA. Here, we present a 3.3 angstrom-resolution cryo-EM structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface comprised of two copies of the catalytic subunit EZH2, which limits nucleosome DNA interaction and occludes H3 tail accessibility to the active site. Our results reveal an unexpected mechanism for RNA-mediated inactivation of a chromatin-modifying enzyme. Furthermore, the flexible loop of EZH2 that helps stabilize RNA binding also facilitates the handoff between RNA and DNA, an activity implicated in PRC2 regulation by RNA.

Activation of automethylated PRC2 by dimerization on chromatin

“…The two PRC2 complexes and the nucleosome form a flexible, tripartite structure stabilized by contacts between the three components (Figure 1). In contrast to other recently described symmetric PRC2 dimers, 17,18 the two PRC2 complexes are arranged asymmetrically, with only one of them contacting the histone octamer in a way that is compatible with H3 methylation. We refer to this PRC2 as nucleosome-proximal PRC2 (PRC2 prox ) (Figure 1A,C, blue).…”

Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing

“…In summary, we showed that LEA proteins is an effective sample protectant for AWI damage in cryo-EM grid preparation. By simply adding AavLEA1 or RvLEAM short to samples before plunge freezing, we were able to determine the cryo-EM structures of both PP and PRC2 at comparable, or better resolution than those previously reported using more challenging and complicated anti-AWI damage strategies 13,34,[37][38][39][40][41][42] . The LEA protein additives provide a simple, robust, and cost-effective anti-AWI damage solution that any cryo-EM labs and facilities in the world can readily incorporate into their existing workflow.…”

Are non‐protein coding RNAs junk or treasure?

“…[32,33] Only recently was a specific mechanism discovered by which RNA G-quadruplexes, often found in long ncRNAs, or lncRNAs, downregulate the ability of the polycomb repressive complex 2 (PRC2) to silence chromatin by installing epigenetic marks on histones. [34] This elemental function of G-quadruplexes maintains gene loci in a transcriptionally active state. Clearly, in this case the absence of evidence did not provide evidence of the absence of function.…”

“…The results of the project showed that an elemental function of many ncRNAs is the binding of specific transcription factors. [ 6 ] As the example of PRC2 indicates, [ 34 ] such binding of specific protein factors can profoundly affect transcription levels, although finding a specific phenotype for such an ncRNA will take time. In fact, genetically deleting an ncRNA may not immediately lead to an observable phenotype.…”