This Science Short, written by Jailynn Harke, summarizes the findings of: Harke, J., Lee, J.R., Nguyen, S.C., Arab, A., Rakowiecki, S.M., Hugelier, S.,…& Joyce, E.F. (2024). Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain. Molecular Cell 84 (24). https://doi.org/10.1016/j.molcel.2024.10.042.
Each one of us begins as a single cell - when sperm meets egg. That cell divides into two, then those two into four, so-on and so-forth until there are trillions of cells, and a human being. Every one of those cells carries the same blueprint in the form of DNA. As cells divide though, they make decisions about whether to become a skin cell or a liver cell, etc. Different cell fates are, in part, determined by certain pieces of the DNA (genes) being decommissioned while others are actively ramped up for expression. The pieces of DNA directing whether a gene is ramped up are called “enhancers”. One reason we have so many different types of cells is because the enhancers can fine-tune where and when each target gene is activated. They’re like the conductor of an orchestra, quieting the winds to let the French horn be heard. Under normal conditions, the enhancers communicate well with their target genes, and a healthy human results. However, a miscommunication early on in development can be lethal if severe enough or result in a malformation. Gone awry later in life, cancers can develop. While we have these and other examples that demonstrate the importance of enhancer communication, we still don’t fully understand how it’s effectively carried out within the cell.
Our recent publication set out to visualize enhancer communication in 3-D using state-of-the-art microscopes, each with an experiment designed to peel back the layers of enhancer communication from the large-scale down to finer resolution. We first measured the size (i.e. volume) of an entire chunk of DNA, with several enhancers and a target gene, in cells that had active enhancer communication and cells that did not. We didn’t find any differences, but we could tell that the structure was very compact in comparison to another chunk of DNA. Next, we divided the large chunk into 32 smaller pieces and imaged those one-by-one. By imaging in this sequential manner, it was like connecting the dots. We could then chart if the active enhancers were closer to the target gene than inactive enhancers. To our surprise, all the enhancers were very close to the target gene, and we could only see subtle shifts between the connected dots. I pictured the data like a water balloon being squeezed – if the DNA was inside the water balloon, it was all close together, but you could change what was interacting with what in subtle ways by squeezing the outside.
Since we weren’t detecting differences between cells with active communication and those without, we began to think of the structure as semi-fixed. Still fluid in the sense that the interactions could change slightly but not dramatically across the tissue. This could be convenient if you’re an enhancer searching for your target gene during development when cells are rapidly dividing, and fates are being decided. Everything is nearby so you don’t have to search too far. Our final experiments determined two factors that played a role in the semi-fixed and compact structure and enhancer communication. The first factor had more of a structural role while the second had more of an effect on communication with the gene. However, both were required for the complete picture. We likened this to two-factor authentication. In the same way you login to something secure, like a bank account, you first put in your credentials and then you receive a confirmation number via text message. Both pieces of information are required to login. Enhancer communication seems to not be so different: the structure is compact and waiting but the additional enhancer signal must be received for the gene to be effectively targeted.
Jailynn Harke is an active postdoctoral research fellow at the University of Pennsylvania. Outside of the lab, she spends her time on the trails of Wissahickon Valley Park with her husband and two dogs, and at the gym with friends.