A protein that masterminds the way DNA is wrapped within chromosomes has a major role in the healthy functioning of blood stem cells, which produce all blood cells in the body, according to a new study from researchers at Weill Cornell Medicine.

The protein, known as histone H3.3, organizes the spool-like structures around which DNA is wrapped in plants, animals and most other organisms. Histones enable DNA to be tightly compacted, and serve as platforms for small chemical modifications – known as epigenetic modifications – that can loosen or tighten the wrapped DNA to control local gene activity.

The study, which appeared Dec. 27 in Nature Cell Biology, examined H3.3’s role in blood stem cells, also known as hematopoietic stem cells (HSCs), that are a major focus of efforts to develop stem-cell-based medicine. Normally most HSCs stay in a stem-like, uncommitted state where they can survive long-term, slowly self-renewing, while some HSCs mature or “differentiate” to produce all the different lineage-specific blood cell types.

The study found that H3.3 is crucial for both processes; deleting the protein from HSCs led to reduced HSC survival, an imbalance in the types of blood cell produced by the HSCs and other abnormalities.

“How hematopoietic stem cells coordinate their self-renewal and differentiation into various blood cell types in a balanced way has been a mystery to a great extent, but this study helps us understand those processes much better at the molecular level and gives us many new clues to pursue in further investigations,” said study co-senior author Dr. Shahin Rafii ’82, director of the Ansary Stem Cell Institute, chief of the Division of Regenerative Medicine and the Arthur B. Belfer Professor in Genetic Medicine at Weill Cornell Medicine.

The study was a collaboration that also included co-first and co-senior authors Ying Liu, Ph.D. ’15, and Peipei Guo, Ph.D. ’16,senior instructors in the Rafii Laboratory; co-senior author Duancheng Wen, assistant professor of reproductive medicine research in obstetrics and gynecology; and co-author Steven Josefowicz, assistant professor of pathology and laboratory medicine and a member of the Sandra and Edward Meyer Cancer Center, all of Weill Cornell Medicine.

HSCs are among the most studied stem cells because of their importance in health and disease, and their potential in regenerative medicine. A single HSC can give rise to all blood cell types, from red blood cells and platelets to T cells, B cells and pathogen-engulfing macrophages. A more precise understanding of how HSCs work could lead to many applications including lab-grown blood for transfusions, and better HSC transplants for cancer patients.

H3.3 also has been a major focus of interest for biologists in recent years, as evidence of its importance in HSCs and other stem cells – and its role in various cancers when mutated – has mounted. But just what histone H3.3 does in HSCs, and in other cell types where it appears, has been far from clear.

“Added to the complexity of this project, is that two different genes (H3.3A and H3.3B) code for the same H3.3 protein,” Wen said. “Therefore, we had to painstakingly delete both genes in mice by genetic engineering, a herculean task that required a great deal of genetic manipulation of stem cells.”

“Our powerful mouse model allows inducible and complete deletion of the H3.3 protein in all organs, or specific types of organs, at selected developmental stage of a mouse,” said Liu, who’s also a research associate in Rafii’s lab. “Employing this approach, we showed that H3.3’s absence in adulthood primarily causes a depletion of the long-term, self-renewing HSCs on which future blood-cell production depends.

“Most importantly,” she said, “we found evidence that H3.3 has its effects on HSCs in part by anchoring several key epigenetic marks at developmental genes and endogenous retroviruses (ERVs), which are remnants of viruses that once inscribed themselves into our distant evolutionary ancestors’ DNA.”

The team now plans further studies, in HSCs and other cell types, to understand in more detail how H3.3 exerts its effects and what happens when it is absent. More importantly, developing approaches to monitor the H3.3 command of the epigenetic landscape could enable them to more effectively increase blood production.

A version of this story appears on the Weill Cornell Medicine website.

Jim Schnabel is a freelance writer for Weill Cornell Medicine.