1 April 2022

Learning from the single cell: a new technique to unravel gene regulation

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How is the activity of genes regulated by the packaging of DNA? To answer this question, Franka Rang and Kim de Luca, researchers from the group of Jop Kind (group leader at the Hubrecht Institute and Oncode Investigator), developed a technique to measure both gene activity and DNA packaging at the same time. This method, EpiDamID, determines the location of modified proteins around which the DNA is wrapped. It is important to gather information about these modifications, because they influence the accessibility of DNA, thus gene activity. EpiDamID is therefore valuable for research into the early development of organisms. The results of the study are published in Molecular Cell on April 1st 2022.

In order to fit DNA into the nucleus of a cell, it is tightly packed around nuclear proteins: histones. Depending on the tightness of this winding, the DNA can be (in)accessible to other proteins. ThisĀ  determines whether gene expression, translation of DNA into RNA and eventually into proteins, can take place.

DNA packaging determines gene activity

The tightness of DNA winding around histones is regulated by the addition of molecular groups to the histones. For example, these so-called post-translational modifications (PTMs) can loosen the DNA winding. This makes the DNA better accessible for certain proteins and enables gene expression. In turn, the proteins involved in this process directly recognize and bind the PTMs. This enables transcription: the process of DNA copying.

The regulation of gene expression, for instance through PTMs, is also known as epigenetic regulation. Since all cells in a body have the same DNA, it is crucial to regulate gene expression to (de)activate specific functions in individual cells. For instance, heart muscle cells have different functions than skin cells, thus require different genes to be expressed.

Analysis of single cells using EpiDamID

To understand how PTMs affect gene expression, first authors Franka Rang and Kim de Luca designed a new method to determine the location of the modifications. Using this approach, called EpiDamID, researchers can analyze single cells, whereas previous methods were only able to measure a large group of cells. Analysis on such a small scale provides knowledge on how DNA winding differs per cell, rather than information on the average DNA winding of many cells.

EpiDamID is based on DamID, a technique which is used to determine the binding location of certain DNA-binding proteins. Using EpiDamID, the binding location of specific PTMs on histone proteins can be detected in single cells. Compared to others, a great advantage of this technique is that researchers need very limited material. Furthermore, EpiDamID can be used in combination with other methods, such as microscopy, to study regulation of gene expression on different levels.

Future prospects

Following the development of this technique, the Kind group will focus on the role of PTMs from the point of view of developmental biology. Because researchers can analyze single cells using EpiDamID, they need only a limited amount of material to obtain enough data. This allows researchers to study the early development of organisms from its first cell divisions, when the embryo consists of only a few cells.


Rang, F. J.*, de Luca, K. L.*, de Vries, S. S., Valdes-Quezada, C., Boele, E., Nguyen, P. D., Guerreiro, I., Sato, Y., Kimura, H., Bakkers, J. & Kind, J. Single-cell profiling of transcriptome and histone modifications with EpiDamID. Molecular Cell, 2022.

*Authors contributed equally

Image Kind



Jop Kind is group leader at the Hubrecht Institute and Oncode Investigator.