Researchers at New York University have created artificial Hawks genes – which plan and direct where cells go to develop tissues or organs – using new synthetic DNA technology and genome engineering in stem cells.
Their findings, published in scienceconfirm how clusters of Hawks genes help cells learn and remember where they are in the body.
Hawks genes as architects of the body
Almost all animals—from humans to birds and fish—have an anteroposterior axis, or a line that runs from head to tail. During development, Hox genes act as architects, setting the blueprint for where cells go along the axis as well as what parts of the body they make up. Hawks genes ensure that organs and tissues develop in the right place, forming the thorax or placing the wings in the correct anatomical positions.
If Hawks genes fail due to misregulation or mutation, cells can be lost, which plays a role in some cancers, birth defects and miscarriages.
“I don’t think we can understand development or disease without understanding Hawks genes,” said Esteban Mazzoni, associate professor of biology at NYU and co-senior author of the study.
Despite their importance in development, Hawks genes are hard to study. They are tightly organized in clusters, only with Hawks genes in the part of the DNA where they are found, and no other genes around them (what scientists call a “gene desert”). And while many parts of the genome have repetitive elements, Hawks clusters have no such repeats. These factors make them unique but difficult to study with conventional gene editing without affecting neighboring ones Hawks genes.
Starting over with synthetic DNA
Can scientists create artificial Hawks genes to better study them instead of relying on gene editing?
“We’re very good at reading the genome or sequencing DNA. And thanks to CRISPR, we can make small edits to the genome. But we’re still not good at writing from scratch,” Mazzoni explained. “Writing or building new parts of the genome can help us test for sufficiency—in this case, find out which smallest unit of the genome a cell needs to know where it is in the body.”
Mazzoni teamed up with Jef Boeke, director of the Systems Genetics Institute at NYU Grossman School of Medicine, who is known for his work on synthesizing a synthetic yeast genome. Boeke’s lab wanted to translate this technology into mammalian cells.
Graduate student Sudarshan Pingley in Boke’s lab made long strands of synthetic DNA by copying DNA from Hawks rat genes. The researchers then delivered the DNA to a precise location in pluripotent stem cells from mice. Using different species allowed the researchers to distinguish between synthetic rat DNA and natural mouse cells.
“Dr. Richard Feynman famously said, ‘What I cannot create, I do not understand.’ We are now a huge step closer to understanding Hawks” said Bouquet, who is also a professor of biochemistry and molecular pharmacology at NYU Grossman and co-senior author of the study.
Studying Hawks clusters
With the artificial Hawks DNA in mouse stem cells, researchers can now study how Hawks genes help cells learn and remember where they are. In mammals, Hawks clusters are surrounded by regulatory regions that control how Hawks genes are activated. It was not known whether the cluster alone or the cluster plus other elements were required for cells to learn and remember where they were.
The researchers found that these gene-dense clusters alone contain all the information cells need to decode a positional signal and remember it. This suggests that the compact nature of Hawks clusters is what helps cells learn their location, confirming a long-standing hypothesis that Hawks genes that were previously difficult to test.
The creation of synthetic DNA and artificial Hawks genes pave the way for future research on animal development and human disease.
“Different species have different structures and shapes, many of which depend on how Hawks clusters are expressed. For example, a snake is a long thorax with no limbs, while a skate has no thorax and is only limbs. A better understanding of Hawks clusters can help us understand how these systems adapt and modify to create different animals,” Mazzoni said.
“More broadly, this synthetic DNA technology, for which we’ve built something of a factory, will be useful for studying diseases that are genomically complex, and we now have a method to produce much more accurate models of them,” Bocke said.
This work was supported in part by the National Institutes of Health (grants RM1HG009491, R01AG075272, R01NS100897, R01GM127538, and F32CA239394), New York State Stem Cell Science (C322560GG), and the Melanoma Research Foundation (687306).