Experts build artificial Hox genes using new synthetic DNA technology

Using cutting-edge synthetic DNA technology and genomic engineering in stem cells, scientists at New York University have created artificial Hox genes, which regulate and direct where cells go to develop tissues or organs.

Their research, which was published in Science, supports how Hox gene clusters assist cells in learning and remembering their location within the body.

Hox genes as architects of the body

An anterior–posterior axis, or a line that extends from head to tail, is a feature shared by almost all animals, including humans, birds, and fish. Hox genes serve as architects during development, laying out the blueprint for where cells will go along the axis and what body parts they will form. Hox genes control where organs and tissues grow, forming the thorax or giving wings their proper anatomical placement.

Hox genes can malfunction due to dysregulation or mutation, leading to cell loss that can contribute to certain cancers, birth defects, and miscarriages.

I don’t think we can understand development or disease without understanding Hox genes.”

Esteban Mazzoni, Study Co-Senior Author and Associate Professor, Biology, New York University

Despite being crucial for development, Hox genes are difficult to research. Hox genes are the only genes present in the region of DNA where they are found, forming what scientists refer to as a “gene desert” around them. They are tightly arranged in clusters.

Additionally, Hox clusters lack the repetitive elements found in many other regions of the genome. These characteristics make them distinct, but they also make them challenging to study using traditional gene editing without affecting nearby Hox genes.

Starting anew with synthetic DNA

Is it possible for researchers to develop artificial Hox genes to better investigate them, rather than relying on gene editing?

We are very good at reading the genome, or sequencing DNA. And thanks to CRISPR, we can make small edits in the genome. But we’re still not good at writing from scratch. Writing or building new pieces of the genome could help us to test for sufficiency—in this case, find out what the smallest unit of the genome is necessary for a cell to know where it is in the body.”

Esteban Mazzoni, Study Co-Senior Author and Associate Professor, Biology, New York University

Mazzoni collaborated with Jef Boeke, who is recognized for his work—in creating a synthetic yeast genome. Jef Boeke serves as the director of the Institute of System Genetics at the NYU Grossman School of Medicine. The goal of Boeke’s lab was to apply this technology to mammalian cells.

By replicating DNA from the rat Hox genes, graduate student Sudarshan Pinglay created long strands of synthetic DNA in Boeke’s lab. The DNA was then implanted precisely into mouse pluripotent stem cells by the researchers. Using distinct species enabled the investigators to differentiate between the synthetic rat DNA and the natural cells of mice.

Dr. Richard Feynman famously opined, ‘What I cannot create, I do not understand.’ We are now a giant step closer to understanding Hox.”

Jef Boeke, Study Co-Senior Author and Director, Institute of System Genetics, NYU Grossman School of Medicine

Boeke, is also a professor of biochemistry and molecular pharmacology at NYU Grossman.

Studying Hox clusters

The scientists could now investigate how Hox genes assist cells in learning and remembering their location, thanks to the synthetic Hox DNA present in mouse stem cells. In mammals, regulatory regions that manage the activation of the Hox genes surround Hox clusters. It was unclear whether the cluster was necessary for the cells to learn and remember their location on its own or in combination with other components.

The researchers found that these gene-dense clusters alone hold all of the data required for cells to decode and remember a positional signal. This supports a long-held theory about Hox genes that were previously challenging to test, according to which the compact nature of Hox clusters is what aids cells in learning their location.

The development of synthetic DNA and artificial Hox genes sets the stage for future research on animal development and human diseases.

Mazzoni remarks, “Different species have different structures and shapes, a lot of which depends on how Hox clusters get expressed. For instance, a snake is a long thorax with no limbs, while a skate has no thorax and is just limbs. A better understanding of Hox clusters may help us to understand how these systems get adapted and modified to make different animals.”

Boeke adds, “More broadly, this synthetic DNA technology, for which we have built a kind of factory, will be useful for studying diseases that are genomically complicated and now we have a method for producing much more accurate models for them.”