New research methods from the EU are using pulsing lasers to illuminate the fleeting interactions between the countless number of proteins and DNA that together make up an organism’s epigenome. Unlike previous efforts to study the epigenome, this technology promises to offer greater resolution and precision for understanding how cells interpret the entirety of the genome for their specific needs.
At the point of conception, the union of egg and sperm cells together create a complete set of DNA that contains all the information needed to instruct a single cell to grow up into a mature, conscious adult. In humans, all this genetic information is spelled out in about three billion base pairs of DNA, which are organized into 23 pairs of chromosomes. Together, this complete genetic blue print is called a “genome.”
Though most human cells contain complete copies of the genome in their cell nuclei, no individual cell needs all the information that that genome contains. Just as a single person does not need to become familiar with all the information contained within a phonebook, a single cell does not need to read all 3 billion base pairs of DNA. For example, neurons do not need to know how to contract like cells in the heart, and cells in the lungs do not need to know how to secrete calcified matrices for bone development. Instead, interactions between DNA and proteins help indicate to a cell what parts of the genome are specific to that cell’s needs. The DNA and protein interactions that regulate the way in which the open genome “book” is selectively read and interpreted is referred to holistically as the “epigenome.”
Previous research into the epigenome involved the laborious process of examining the binding abilities of different proteins to different segments of DNA. However, this method is limited because the binding process between DNA and protein can take hours to produce clear results. This means that in addition to being slow to yield results, the resulting data only reveals information about binding that occurs over a long time interval. Up to now, DNA-protein binding that is more fleeting has remained an unturned stone.
However, research from the EU-funded Applied Technology for Language-Aided CMS (ATLAS) program has potentially just accelerated the rate at which future discoveries about the epigenome will be made. Their novel methodology involves exposing DNA and proteins to laser beams of light that pulse on for intervals lasting only one femtosecond long (one millionth of one billionth of a second). These short time intervals allow for the illumination of the interactions between DNA and proteins in great detail—much like a high-speed camera that can capture images of a speeding bullet. The brief light exposure causes the DNA and proteins to bind fleetingly to each other and reveal the different roles that different proteins play in the epigenome.
The new technology is quite exciting and applicable to virtually all branches of the life sciences. In addition to offering a fresh, precise look at DNA-protein interactions, the laser-pulse system also requires very little starting material to produce results. Perhaps, the most exciting aspect is that the system can be automated. Much like human understanding of the genome increased dramatically after the invention of automated DNA sequencing machines, a deluge of information may be at hand about the epigenome.
By Sarah Takushi