DNA methylation for precise gene expression regulation

If the genome is viewed as a guidebook for how a cell should operate, then annotations, highlights, and bookmarks are included on every page. Several of these markers’ functions are still unclear; do they serve as active cues to guide the reader to the appropriate pages at the appropriate times, or do they just serve as a record of the pages the reader has previously seen?

DNA methylation for precise gene expression regulation
Scientific illustration of a chromatin close-up. A portion of the chromatin is shown as open, allowing for transcription factors to bind to DNA (lilac spheres). Depending on whether the DNA is methylated or not (white spheres), transcription factors have different sensitivities that affect their function. Image Credit: Joana Gomes Campos de Carvalho/EMBL

The survival and functionality of the cell could be significantly impacted by this minute variation in its cellular language. One such annotation, DNA methylation, exerts a very selective layer of control on the expression of genes, one that changes depending on cell type and destiny, as researchers from the Krebs group at EMBL Heidelberg have recently demonstrated.

What is DNA methylation?

A suppressive epigenetic change is DNA methylation. In mammalian cells, it can be present in certain DNA sequences where enzymes change the cytosine base’s structure gradually by adding a tiny chemical group termed “methyl.”

It is crucial for the development of mammals and plays a significant part in the regulation of genomic activity. Silencing, a procedure that stops the expression of genes, is one of its crucial roles. A durable imprint on DNA called methylation can be passed down through many generations of cells and even entire species.

In the aforementioned analogy, the annotations, highlights, and bookmarks stand in for what are known as “epigenetic marks,” and the “reader” is often the intricate molecular machinery that regulates gene expression. The second group contains specialized proteins referred to as transcription factors.

The area around a specific portion of DNA goes through physical and chemical changes when it has to be expressed, making it more receptive to such molecular machinery. Although DNA methylation is present across the genome, it is still unclear if and how it impacts accessibility at certain genomic regions.

Our group is interested in the fundamental mechanisms that regulate gene expression. We are particularly interested in cis-regulatory elements like enhancers—DNA regions that control the activity of genes.

Arnaud Krebs, Group Leader, Genome Biology Unit, European Molecular Biology Laboratory

While DNA methylation is frequently decreased in active enhancers, the cause-effect relationship between the two is still unknown, which attracted Krebs’ team. Does demethylation occur as a result of these DNA regions being activated? Or does the activation originate from the decrease in methylation?

The scientists employed single-molecule footprinting, a high-resolution method created in their lab, to look into this. They were able to detect DNA methylation, accessibility, and transcription factor binding at the level of individual DNA molecules using this technique.

They used this throughout the whole genome in various cell types, including differentiated cells and mouse embryonic stem cells. The scientists were able to comprehend DNA methylation’s function in gene regulation in a living cell more thoroughly due to this scale and resolution combination.

The researchers discovered that while roughly 97% of the enhancers they examined were accessible regardless of DNA methylation, about 3% were only active in the absence of DNA methylation.

Methylation at these sites decreased DNA accessibility and directly interfered with transcription factor binding. These methylation-sensitive enhancers took different forms in various cell types and developmental stages.

The 3% of enhancers that seem to be regulated by DNA methylation are enriched for cell-type specific enhancers. We think they are connected to genes that are important for cellular identity.

Elisa Kreibich, Study First Author and PhD Student, European Molecular Biology Laboratory

The study was published in the journal Molecular Cell.

Krebbs added, “By making our measurements at the level of single molecules, we can figure out the connections and interactions between the layers of gene regulation that exist in a cell. While DNA methylation has often been used as a marker for cellular processes, including those involved in cancer, our study shows where it is truly instructive, rather than simply indicative.

Scientists from all across the world can now utilize the tools and analytical codes the team employed as they are made openly available by the team.

Journal reference:

Kreibich, E., et al. (2023). Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Molecular Cell. doi.org/10.1016/j.molcel.2023.01.017


The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of AZoLifeSciences.
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