Learning from the single cell: a new technique


image: zebrafish notochord nuclei at the 15-somite stage. Gray: nuclear DNA (DAPI). Colour: histone H3K9me3
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Credit: Phong Nguyen, Franka Rang and Kim de Luca. Copyright Hubrecht Institute.

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

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

DNA packaging determines gene activity

The tightness of DNA wrapping around histones is regulated by the addition of molecular groups, called post-translational modifications (PTM), to histones. For example, if certain molecules are added to histones, the winding of DNA is loosened. This makes the DNA more accessible for certain proteins and causes the genes of that part of the DNA to turn on, or Express. Moreover, proteins crucial for gene expression can directly recognize and bind PTMs. This allows transcription: the process of copying DNA.

The regulation of gene expression, for example via PTMs, is also known as epigenetic regulation. Since all cells in a body have the same DNA, regulation of gene expression is necessary to (de)activate specific functions in individual cells. For example, heart muscle cells have different functions than skin cells and therefore require the expression of different genes.

Single cell analysis using EpiDamID

To understand how PTMs affect gene expression, first authors Franka Rang and Kim de Luca devised a new method to determine the location of the changes. Using this approach, called EpiDamID, researchers can analyze single cells, whereas previous methods could only measure a large group of cells. Such a small-scale analysis provides insight into how DNA coiling differs from cell to cell, rather than gaining insight into the average DNA coiling of many cells.

EpiDamID is based on DamID, a technique 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 big advantage of this technique is that researchers need very limited equipment. Additionally, EpiDamID can be used in combination with other methods, such as microscopy, to study the regulation of gene expression at different levels.

Future prospects

Following the development of this technique, the Kind group will focus on the role of PTMs from a developmental biology perspective. Since single cells are analyzed using EpiDamID, only a limited amount of hardware is needed to generate 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.



Rank, FJ*, de Luca, KL*, de Vries, SS, Valdes-Quezada, C., Boele, E., Nguyen, PD, 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

Jop Kind is a group leader at Hubrecht Institute for Developmental Biology and Stem Cell Research and Oncode Investigator.

About the Hubrecht Institute

The Hubrecht Institute is a research institute focused on developmental and stem cell biology. It comprises 21 research groups that carry out fundamental and multidisciplinary research, both in healthy systems and disease models. The Hubrecht Institute is a research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), located in the science park of Utrecht. Since 2008, the institute has been affiliated with UMC Utrecht, advancing the translation of research to the clinic. The Hubrecht Institute has a partnership with the European Molecular Biology Laboratory (EMBL). For more information, visit http://www.hubrecht.eu.

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