PRC2 and RNA: Decoding the Epigenetic Puzzle in Cancer

The polycomb group (PcG) of proteins have been shown to be crucial in early development and adulthood through their spatial expression and its ability to modify chromatin. PRC2 or Polycomb repressive complex 2  is a protein complex of PcG group of protiens, PRC2, which modifies the chromatin to maintain the genes in their repressive state during development, has been reported to be dysregulated in several cancer types- it has both oncogenic and tumor suppressive functions. PRC2 catalyses the methylation of lysine 27 of histones by binding to the CpG islands- H3K27me1, H3K27me2 and H3K27me3. PRC2 complex has multiple subunits like Enhancer of Zeste Homolog 2 (EZH2) or Enhancer of Zeste Homolog 1 (EZH1), Jumonji, AT-rich interactive domain 2 (JARID2), embryonic ectoderm development(EED), Suppressor of Zeste 12 Polycomb Repressive Complex 2 Subunit (SUZ12), Adipocyte Enhancer Binding Protein 2 (AEBP2) and retinoblastoma-associated protein 46 (RBAP46). PRC1 (Polycomb Repressive Complex 1) functions primarily to maintain gene repression by monoubiquitinating histone H2A at lysine 119 (H2AK119ub), which compacts chromatin and inhibits transcriptional activation. It works along with PRC2 to establish and sustain long-term gene silencing essential for development and cell differentiation.

EZH2 is the catalytic subunit of PRC2 responsible for the trimethylation of histone H3 at lysine 27 (H3K27me3), leading to gene repression. It plays a crucial role in maintaining stem cell pluripotency, differentiation, and development. Gain Of Function mutation causes amplification and overexpression of PRC2. Point mutation in the PRC2 subunits gene (missense mutation) enhance the catalytic activity of EZH2. In vivo and in vitro studies it was found tat EZH2 overexpression increases metastasis and cell invasion, and prevent DNA damage repair. EZH2 gain of function mutation also causes lymphoma medicated by BCl2 and Myc in mice. Loss of function mutation causes decrease in PRC2 activity and mutations affecting the H3K27 substrate of PRC2 have been found in several types of cancer. These alterations have been found in all of the genes encoding the core members of PRC2, as well as in several genes encoding associated proteins such as JARID2, which indicates that inactivation of PRC2 is a common event in tumours.

Over the past years, emerging discoveries have portrayed the association of RNA (protein-coding and non-coding) with PRC2 as a critical factor in understanding PRC2 function. With PRC2 being a macromolecular complex of interest in development .

In Junk Mail model, the random binding of PRC2 acts as a regulatory checkpoint for genes that escape epigenetic silencing. At actively transcribed genes, RNA binding to PRC2 leads to its eviction from chromatin or functions as a decoy, preventing PRC2 from repressing these regions. The presence of active chromatin marks further reduces PRC2's affinity for chromatin, promoting gene activation. Simultaneously, for genes requiring silencing, PRC2's binding to RNA facilitates its association with chromatin marks, deposited by PRC1, thereby reinforcing gene repression. 

In masking model, PRC2 prefers to bind with transcripts that are exposed and not bound to any other proteins. It explained the binding preferences of PRC2 in vivo where the RNAs compete with each other to bind to PRC2, and thetranscript without any bound proteins have a higher chance to outcompete other RNAs. In Antagonist model, RNA and CpG regions of chromatin competitively bind to the PRC2 complex, high affinity to a quadraplex of RNA when high density of G quadraplexes are located near splicing sites. 

A -repressed genes, regulatory RNA acts as guide help 

PRC2 to locate bind to target chromatin ( expressed chromatin)

B- Interact with nascent RNA being transcribed (repressed Chromatin)

C- the nascent RNA transcription prevents binding of PRC2 to chromatin

D- Steric hindrence with RBP & PRC2

Inhibitors targeting PRC2 histone methyltransferase activity have been developed for tumors with gain-of-function PRC2 or EZH2 overexpression. However, strategies to enhance PRC2 enzymatic activity are still lacking. Venture into this area would hold  therapeutic efficacy in malignancies such as glioma and leukemia. This can be accomplished by interrupting the inhibitory connection between PRC2 and RNA. The G-quadruplex motif or RNA-binding sites in EZH2 and EED may lead to novel therapeutic methods. In vitro studies have revealed that compounds targeting G-quadruplexes can block PRC2:RNA binding, making them a possible anticancer approach.

Antisense oligonucleotides can potentially relieve PRC2's antagonistic interaction with RNA by targeting certain transcripts. RNA mimics of the G-quadruplex can be used to decrease PRC2 catalytic activity. Inhibiting the RNAbinding activity of PRC2 or its target transcripts could improve PRC2's ability to suppress polycomb-target genes, potentially leading to significant advances in epigenetic therapy for cancer patients.

REFERENCE:

• Yan J, Dutta B, Hee YT, Chng WJ. Towards understanding of PRC2 binding to RNA. RNA biology. 2019 Feb 1;16(2):176-84.
• Comet I, Riising EM, Leblanc B, Helin K. Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nature Reviews Cancer. 2016 Dec;16(12):803-10.

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