How are genes regulated by DNA binding? To answer this question, a method for measuring both gene expression and DNA packing was developed by Franka Rang and Kim de Luca, researchers at the Joop Kind Group (leader of the group at the Hubrecht Institute and Investigator Oncod). This method, EpiDamID, determines the location of the altered proteins around which the DNA is wrapped. The collection of information about these changes is important because they affect the availability of DNA and thus affect the activity of genes. EpiDamID is therefore valuable for research in early development of organisms. The results of the study have been published Molecular cell April 1, 2022.
In order for DNA to enter the cell nucleus, it is wrapped tightly around the nucleus proteins: histones. Depending on the severity of this entanglement, DNA may be (in) accessible to other proteins. Therefore, it determines whether the process gene expressionthe translation of DNA into RNA and ultimately into proteins can take place.
DNA packing determines gene activity
The density of DNA packing around histones is regulated by the addition of molecular groups called changes after translation (PTMs), to histories. For example, if certain molecules are added to histones, DNA circulation slows down. This makes DNA more accessible to certain proteins and activates the genes in that part of the DNA, or expressed. Furthermore, proteins that are important for gene expression can directly recognize and bind to PTM. This allows transcription: DNA copying process.
The regulation of gene expression, for example through PTMs, is also known epigenetic regulation. Because all the cells in the body have the same DNA, regulation of gene expression is needed to activate specific functions in individual cells. For example, heart muscle cells have different functions than skin cells, so they require different genes.
Single cell analysis using EpiDamID
To understand how PTMs affect gene expression, early authors Franca Rang and Kim de Luca developed a new method for determining the location of changes. Using this method, called EpiDamID, the researchers were able to analyze single cells, while previous methods could only measure a large group of cells. Analysis on such a small scale leads to the knowledge of how to differentiate the DNA seal in a cell, rather than information about the average DNA flow of many cells.
EpiDamID is based on DamID, a technique used to determine the location of specific DNA binding proteins. Using EpiDamID, the binding location of specific PTMs on histone proteins in single cells can be determined. Compared to others, the great advantage of this technique is that the researchers need very limited material. Furthermore, EpiDamID can be used in combination with other methods, such as microscopy, to study the regulation of gene expression at different levels.
After developing this technique, the Kind team will focus on the role of PTMs from a developmental biology perspective. Because single cells are analyzed using EpiDamID, only a limited amount of material is needed to produce sufficient data. This allows researchers to study the early development of an organism from the initial division of its cells when the embryo is made up of several cells.
Materials by Hubrecht Institute. Note: Content can be edited according to style and length.