A molecular view of PRC1 at work on chromosomes

Scientists led by Jürg Müller at the MPI of Biochemistry reveal the molecular architecture of the gene-silencing complex PRC1 and how it is targeted to genes controlling cell identity.

Researchers at the Max Planck Institute (MPI) of Biochemistry have determined the structure of human Polycomb Repressive Complex 1 (PRC1), a molecular machine that keeps genes switched off in cells where they should not be active. Although the complex was discovered more than 20 years ago, how its components assemble into a functional machine and how this machine interacts with chromosomes have remained unclear. The new study, published in Nature Structural & Molecular Biology, reveals how the four subunits of PRC1 are assembled and provides a molecular snapshot of the complex at work on a chromosome.

In a nutshell:

• PRC1 is a molecular machine that helps keep developmental regulator genes switched off in cells where they should not be active.
• PRC1 is targeted to specific sites on chromosomes, where it modifies histone proteins around which DNA is wrapped.
• Using cryo-electron microscopy, the researchers determined how the four subunits of human PRC1 fit together and how the complex engages its nucleosome substrate.
• Experiments in fruit flies revealed how this architecture is important for PRC1 assembly and activity and how the intact complex is targeted to the genes it regulates.

PRC1 silences genes

All the cells in our body contain the same genetic information, stored in the DNA. Each cell switches on only the genes it needs. One way cells control gene activity is by adding chemical modifications to histones, the proteins around which DNA is wrapped. PRC1 attaches one such modification—a small protein called ubiquitin—to histones at genes that need to be switched off.

The team set out to visualize PRC1 at the atomic level and understand how the complex is assembled, how it interacts with chromosomes and how it is targeted to the genes it regulates.

What does PRC1 look like?

Using cryo-electron microscopy, the researchers determined the molecular structure of PRC1, which consists of four subunits called RING1B, BMI1, PHC2, and CBX7. In the structure, PRC1 is bound to a nucleosome, the basic unit of chromosome organization in which DNA is wrapped around histone proteins.

“Our study shows how the four subunits of PRC1 form a very compact structure in which the different proteins are tightly integrated. We were also able to visualize how PRC1 engages the nucleosome. The structure allowed us to understand how the architecture of the complex controls its assembly and its activity”, explains Maria Ciapponi, joint first author of the study, who led the structural and biochemical work.

The team then asked whether this architecture is also important for PRC1 function in living cells, turning to the fruit fly Drosophila to find out.

"It was exciting to see how our structural findings connect to the function of the complex in a living organism. We found that one part of the Polyhomeotic protein, the fly counterpart of human PHC2, is essential for holding the PRC1 complex together. A different part of the same protein is required to target the intact complex to the genes it regulates. By combining structural and in vivo approaches, we can therefore begin to understand how PRC1 is assembled and how it finds its target genes,” says Martina Cafiso, joint first author of the study, who carried out the genomic and in vivo analyses.

The study builds on decades of research into how Polycomb proteins regulate gene activity.

“Over the years, we have learned a great deal about how Polycomb complexes function during animal development, but what has been missing is a molecular view of how these complexes are built and how they interact with chromosomes to perform their functions. Our study provides this molecular view for canonical PRC1 and connects its architecture to its assembly, enzymatic activity and targeting to genes,” explains Jürg Müller, corresponding author and head of the Chromatin Biology research group at the MPI of Biochemistry.

PRC1 has medical relevance

Mutations in Polycomb proteins are associated with a range of human diseases, and sometimes changing just a single amino acid in one of the PRC1 subunits can cause disease, including severe neurodevelopmental disorders.

“Understanding how such a small change affects the architecture or activity of the complex can be an important first step towards understanding how the mutation causes disease and, ultimately, towards developing new treatments,” says Müller.

“Now that we can visualize the architecture of the complex, it is a bit like being able to look inside a building and understand why replacing one structural element—or removing a single brick—can cause the whole structure to stop working”, Müller concludes.

 

Glossary

Chromosome: A chromosome is a long DNA molecule, together with its associated proteins, that contains an organism’s genes.

Gene expression / gene silencing: The process by which a cell turns a gene "on" (expression) to produce a protein, or "off" (silencing) to keep it inactive.

Cryo-electron microscopy (cryo-EM): A structural biology technique in which rapidly frozen molecules are imaged by electron microscopy to determine their three-dimensional structure at near-atomic resolution.

DNA: stands for deoxyribonucleic acid, the molecule that carries an organism's genetic information.

Histone: are a family of basic proteins that package DNA within the cell nucleus.

Nucleosome: The basic unit of DNA packaging, made of DNA wound around a core of histone proteins.

Ubiquitin: Ubiquitin is a small protein that cells attach to other proteins to regulate their function or stability.

Polycomb proteins: are proteins that help permanently or long-term silence certain genes. They belong to the so-called Polycomb group of gene regulatory proteins. These proteins usually do not act individually, but rather in complexes, primarily PRC1 or PRC2. This makes the DNA less accessible at certain sites. The genes located there are then transcribed less frequently or not at all.

Polycomb Repressive Complex 1 (PRC1): A protein complex that switches off specific genes to help cells maintain their identity.