New regulatory mechanism identified in the chromatin-modifying complex PRC2

An international research team led by Simon Pöpsel (CMMC) has used cryo-electron microscopy and functional assays to demonstrate how the transcriptional regulator PRC2 impacts biochemical changes in chromatin to control gene regulation.

Human cells exhibit a remarkable diversity of shapes and functions, a property that facilitates the complex development of multicellular organisms from a single fertilized egg. However, this plasticity also poses a risk, as it can drive the malignant transformation of healthy into cancerous cells. Central to these processes is the regulation of gene expression, which depends critically on the organization of the genome. Its packaging into chromatin - a dynamic structure that controls access to the genetic code - is essential for turning genes on or off.

An international team of researchers led by Simon Pöpsel, Principal Investigator at the Center for Molecular Medicine Cologne (CMMC) at the University of Cologne, has identified a new mechanism underlying biochemical changes in chromatin that contribute to gene regulation. The results of their collaborative study with the group of Professor Eva Nogales (Professor at the University of California, Berkeley) have been published in the prestigious journal Molecular Cell under the title: Activation of automethylated PRC2 by dimerization on chromatin (doi.org/10.1016/j.molcel.2024.08.025). 

The Polycomb Repressive Complex 2 (PRC2) is a key regulator of chromatin function in cells, helping to control which genes are turned on or off. It does this by chemically changing histone proteins through its enzymatic histone methyltransferase (HMTase) activity. Histones are part of nucleosomes, the basic structure that organizes DNA into chromatin. The catalytic subunit responsible for this activity in PRC2 is called enhancer of zeste homolog 2 (EZH2).

PRC2 is the only known complex to produce a specific mark – the trimethylation of lysine 27 of histone H3 (H3K27me3). This mark is considered a "stop sign" on nucleosomes preventing the activation of specific genes. This regulatory process is of particular significance during development, as it ensures the appropriate genes are either activated or repressed at the right time.

By employing single-particle cryo-electron microscopy (cryo-EM), the researchers were able to visualize a previously unidentified molecular complex between two PRC2 complexes and a nucleosome. The three-dimensional details revealed by this method showed how the two PRC2 complexes work together as a dimer, with one complex stimulating its neighbor for enzymatic activity. Consequently, the activated PRC2 is capable of chemically modifying the nucleosome in a manner that can ultimately result in the silencing of genes.

The researchers could demonstrate several interesting details of this mechanism of activation. First, the activation of one PRC2 within the dimer depends on the recognition of a methylated lysine by the regulatory subunit EED, which is also required for activation in other contexts. Second, in the case of the PRC2 dimer, the EED binding, stimulatory methyl-lysine is part of the active EZH2 subunit of one participating PRC2 itself. It is generated though a self targeting activity called auto-methylation. 

Therefore, in a nutshell, PRC2 can methylate itself and by forming a dimer with a second PRC2 while bound to a nucleosome, be an activator of that complex. In this way, PRC2 can perform enzymatic activation independent of other activators that were preciously known to be required for PRC2 activity. In contrast to the alternative activation processes, dimerization requires the presence of two PRC2 complexes, thereby necessitating a higher local PRC2 concentration. This suggests that the local abundance of PRC2 may play a role in regulating the initial deposition of H3K27me3 by PRC2 dimers.

Supported by further structural and functional analyses, the findings presented in this study underscore the intricate manner in which chromatin regulators integrate cues from the local chromatin environment to enable their targeted and regulated function. Moreover, the mechanism described here illustrates how automethylation and dimerization are integrated by PRC2, showing that mechanisms of auto-catalysis, homo-oligomerization, and allosteric regulation are not confined to the classical examples of kinase autophosphorylation. Instead, they are highly relevant to multi-protein complexes that regulate chromatin function through histone modification.

The study provided insights into the mechanisms of chromatin regulation, uncovering unexpected and exciting data that will inspire future investigations. A comprehensive understanding of the function and regulation of molecules involved in chromatin regulation, which play pivotal roles in human health and disease, represents a crucial foundation for the development of potential disease treatments in the future. 

“By cryo-EM, we can literally see molecules in action at remarkable detail. This project was one of the examples where we saw the three-dimensional structure of a protein-DNA complex and immediately had a ‘Eureka’ moment. The arrangement of molecules directly showed a mechanism of PRC2 regulation and could explain observations that were enigmatic before our structural data”, Dr. Simon Pöpsel explains. “However, the structural data obtained by cryo-EM still required a a lot of effort to validate the observed effects through biochemical and cellular assays. We are extremely happy and grateful to have successfully completed this study after many years of hard work.” 

Pöpsel adds: “These chromatin regulators play pivotal roles in cellular responses to growth and differentiation signals. They are frequently mis regulated or dysfunctional in severe diseases such as cancer. Understanding their structure and mechanisms of function facilitates a more comprehensive understanding of disease processes and the contribution of genetic and epigenetic changes to the pathobiology of human disease.”