Using new synthetic DNA technology and genomic engineering in stem cells, researchers created artificial Hox genes, which plan and direct where cells go to develop tissues or organs. Their findings support the idea that Hox gene clusters help cells learn and remember where they are in the body.
Using new synthetic DNA technology and genomic engineering in stem cells, researchers at New York University created artificial Hox genes, which plan and direct where cells go to develop tissues or organs. Their findings, published in Science, confirm how Hox gene clusters assist cells in learning and remembering where they are in the body.
Hox genes as architects of the body
Almost all animals, from humans to birds to fish, have an anterior-posterior axis, or a line that runs from head to tail. Hox genes act as architects during development, determining where cells go along the axis and what body parts they form. Hox genes ensure that organs and tissues develop in the correct location, such as forming the thorax or positioning wings.
Cells can be lost if Hox genes fail due to misregulation or mutation, and this has been linked to some cancers, birth defects, and miscarriages. “I don’t think we can understand development or disease without understanding Hox genes,” said Esteban Mazzoni, associate professor of biology at NYU and co-senior author of the study.
Despite their importance in development, Hox genes are challenging to study. They are tightly organized in clusters, with only Hox genes in the piece of DNA where they are found and no other genes surrounding them (what scientists call a “gene desert”). And while many parts of the genome have repetitive elements, Hox clusters have no such repeats. These factors make them unique but difficult to study with conventional gene editing without affecting neighboring Hox genes.
Starting anew with synthetic DNA
Instead of using gene editing, could scientists create artificial Hox genes to better study them?
“We excel at reading the genome and sequencing DNA. We can also make small changes to the genome using CRISPR. However, we are still not very good at writing from scratch “Mazzoni elaborated. “Writing or constructing new pieces of the genome could aid us in testing for sufficiency — in this case, determining what the smallest unit of the genome is required for a cell to know where it is in the body.”
Mazzoni collaborated with Jef Boeke, director of the Institute of System Genetics at NYU Grossman School of Medicine and well-known for his work on creating a synthetic yeast genome. Boeke’s lab was looking to translate this technology to mammalian cells.
Sudarshan Pinglay, a graduate student in Boeke’s lab, created long strands of synthetic DNA by copying DNA from rats’ Hox genes. The DNA was then delivered to a specific location within mouse pluripotent stem cells. The researchers were able to distinguish between synthetic rat DNA and natural mouse cells by using different species.
“What I cannot create, I do not understand, famously stated Dr. Richard Feynman. We’ve come a long way toward understanding Hox “said Boeke, who is also a professor of biochemistry and molecular pharmacology at NYU Grossman and a co-senior author on the study.
Studying Hox clusters
Researchers can now investigate how Hox genes help cells learn and remember where they are using artificial Hox DNA in mouse stem cells. Hox clusters in mammals are surrounded by regulatory regions that regulate how Hox genes are activated. It was unclear whether the cluster alone or the cluster in combination with other elements was required for the cells to learn and remember where they were.
The researchers discovered that these gene-dense clusters alone contain all of the information needed for cells to decode and remember a positional signal. This suggests that the compact nature of Hox clusters is what helps cells learn their location, confirming a long-standing hypothesis on Hox genes that was previously difficult to test.
The development of synthetic DNA and artificial Hox genes opens the door to future studies on animal development and human diseases. “Different species have different structures and shapes, which are heavily influenced by how Hox clusters are expressed. A snake, for example, has a long thorax but no limbs, whereas a skate has no thorax and only limbs. A better understanding of Hox clusters could help us understand how these systems adapt and change to produce different animals “Mazzoni stated.
“More broadly, this synthetic DNA technology, for which we have built a kind of factory,” said Boeke, “will be useful for studying diseases that are genomically complicated, and we now have a method for producing much more accurate models for them.”
