Role of nitric oxide in controlling genetic regulators to maintain cellular health

When you think of gases involved in your health, oxygen probably tops the list. But there’s another gas, nitric oxide, that quietly plays a crucial role in keeping your body running smoothly. Though it might sound like something from a chemistry lab, nitric oxide is made right inside your body. In fact, the discovery of this gaseous molecule led to the Nobel Prize in Physiology or Medicine in 1998 to Dr Robert F Furchgott, Dr Louis J Ignarro, and Dr Ferid Murad for their discoveries concerning nitric oxide as a signaling molecule in the cardiovascular system. However, we are still far from understanding the complex set of regulations this gaseous molecule governs, and Scientists are still uncovering how deeply it’s involved in cellular health.

In our recent study published in Nature Communications (1), we explored how this tiny, simple molecule interacts with proteins inside endothelial cells, the cells that line your blood vessels. What we found opens a new window into how nitric oxide helps regulate key proteins that maintain the health and balance of your vascular system. At the heart of this discovery is a protein called EZH2, and a chemical process called S-nitrosylation.

The central player: Nitric oxide
Nitric oxide is a short-lived gas that your body naturally produces. It plays an essential role in many bodily functions—from helping your blood vessels relax and widen, to controlling how cells communicate, move, and even defend themselves.

One of nitric oxide’s lesser- known talents is its ability to chemically modify proteins. It does this through a process known as S-nitrosylation, where it attaches to specific parts of a protein, namely, to a sulfur-containing amino acid called cysteine. Think of it as adding a tiny “tag” to the protein, which can change the protein’s function, stability, or location in the cell.

Meet EZH2: The genetic regulator
One of the proteins affected by S-nitrosylation is Enhancer of Zeste Homolog 2 (EZH2). EZH2 is a gene regulator. It’s part of a group of proteins called the Polycomb Repressive Complex 2 (PRC2 com- plex), which works like a dimmer switch to turn down the activity of certain genes. EZH2’s main job is to add a chemical marker, known as H3K27me3 to histones, the spool-like proteins around which DNA is wrapped. This mark tells the cell to keep that section of DNA quiet, preventing the genes in that area from being expressed. Proper control of these genes is essential for normal cell function and health, particularly in endothelial cells, which constantly respond to changing blood flow, pressure, and chemical signals.

A new layer of control: S-Nitrosylation of EZH2 Our research shows that nitric oxide can attach to specific cysteine sites on EZH2, changing how it behaves inside the cell. We found two important sites where this happens:

◆ Cysteine 329: When nitric oxide modifies this residue through S-nitrosylation, EZH2 becomes unstable. It no longer functions properly and starts to break down.

◆ Cysteine 700: In contrast, when this residue is S-nitrosy- lated by nitric oxide, EZH2 loses its ability to add the H3K27me3 mark, essentially shutting down its gene-silenc- ing function.

This is a big deal because it means nitric oxide can turn off EZH2 in two different ways— by making it unstable or by di- minishing its function.

So what does this mean for the cell?
Several important things happen when EZH2 gets modified by nitric oxide:

◆ The PRC2 complex falls apart. Normally, EZH2 works with its partner pro- tein, SUZ12, to form PRC2. But when EZH2 is S-nitrosylated, it can’t hold on to SUZ12 properly. This causes the complex to break apart early, which reduces the gene-silencing H3K27me3 marker.

◆ EZH2 is kicked out of the nucleus. After losing its func- tion, EZH2 moves out of the nucleus (where DNA lives) into the cell’s cytoplasm.

◆ EZH2 gets destroyed. Once in the cytoplasm, EZH2 is marked for degradation. It’s tagged with ubiquitin, a small molecule that tells the cell’s waste-disposal system to break it down. In short, nitric oxide effectively shuts down EZH2, making it unable to silence genes and trigger- ing its removal from the cell.

Why does this matter?

This whole process turns out to be very important for endothelial homeostasis—a term that means the overall balance and healthy functioning of the cells lining our blood vessels. These cells need to adapt constantly to mechanical stress, inflammation, and signals from other parts of the body. EZH2 helps keep certain genes turned off so the cells don’t overreact or go haywire. But under certain conditions such as oxidative stress or inflammation, it’s helpful to reduce EZH2 activity. That’s where nitric oxide steps in, offering a smart way for the cell to fine-tune its genetic control systems in real time. Our study shows that this nitric oxide driven mechanism works not just under healthy conditions, but also during pathological (disease-related) states.

Molecular simulations add insight
To better understand why SUZ12 and EZH2 break up when EZH2 is S-nitrosylated, we used molecular dynamics simulations—computer models that mimic how molecules move and interact. These simulations revealed that S-nitrosylation alters the shape of EZH2’s SAL domain, a region critical for binding SUZ12. When this domain is modified, SUZ12 simply can’t latch on properly anymore, leading to the breakdown of the PRC2 complex.

Looking ahead

This study brings new clarity to how nitric oxide regulates cell behavior through precise protein modifications. We now understand that NO doesn’t just relax blood vessels, it actively rewires how genes are controlled in endothelial cells by modifying a key player like EZH2. The implications of this are wide-ranging. These findings are important because problems with blood vessel stability can lead to many diseases, including heart attacks and strokes. By understanding these mechanisms better, future therapies could be developed to keep blood vessels healthier for longer.

Reference

1. Sakhuja A, Bhattacharyya R, Katakia YT, Ramakrishnan SK, Chakraborty S, Jayakumar H, Tripathi SM, Pandya Thakkar N, Thakar S, Sundriyal S, Chowdhury S, Majumder S. S- nitrosylation of EZH2 alters PRC2 assembly, methyltrans- ferase activity, and EZH2 stabil- ity to maintain endothelial homeostasis. Nat Commun. 2025 Apr 27;16(1):3953.