19 June 2022

Enhancers recruit DNA looping machinery to activate genes

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In their aim to decipher the functioning of our DNA, researchers from the group of Wouter de Laat discovered that specialized sequences in non-coding DNA, called enhancers, recruit a DNA looping machinery to contact and activate genes elsewhere on chromosomes. The results were published in Nature Structural & Molecular Biology on 16 June 2022.

Genes and our genome
Our genome The complete set of DNA or genetic material in a cell. is composed of 23 pairs of chromosomes that collectively contain the genetic information that we inherited from our parents. Chromosomes are extremely long stretches of DNA sequences. Segments of these DNA stretches are genes that encode RNA and protein, the products that give shape and function to our cells and bodies. A fascinating aspect of human biology is the fact that genes only make up 2% of our genome. The rest, 98% of the DNA sequences, is non-coding. Still, these large gene deserts in our chromosomes serve important roles. They contain small sequence segments -known as enhancers- that regulate which gene is transcribedA gene that is transcribed is active. The combination of active genes in a cell determines, amongst other things, the function, shape and size of the cell. in which cell and at what time in development, thereby affecting for instance whether cell becomes a skin cell or a muscle cell. While our genome contains roughly 22.000 genes, it contains millions of these enhancers, some of which can activate genes over large chromosomal distances. This makes the regulation of which genes are active and which are not very complex.

DNA looping
Enhancers have been studied for decades now, and we have a reasonable but still incomplete understanding how they activate gene transcription. An important and still open question is how enhancers can control the transcription of genes that are located at large distances from the enhancers, elsewhere on the chromosome. In the past, the De Laat research group provided the first evidence for DNA looping taking place between enhancers and genes, which brings them in close proximity for gene activation. Recent years have revealed that the protein complex cohesin is the key machinery to create these DNA loops. Cohesin does this by binding the DNA and pulling it out in a loop, a process that constantly takes place everywhere in our genome. This leads to our chromosomes being subdivided in dynamically changing small DNA loops.

The key findings of this work
In the current study, PhD student Niels Rinzema with help of many colleagues from the De Laat group took an original approach to further investigate long-range gene regulation by enhancers. They used CRIPSR-Cas DNA editing technologyA technique that researchers can use to cut the DNA in a very specific place, to make a change there. This way, researchers can study the effect of a specific change in the DNA. to introduce a gene, an enhancer and a so-called insulator sequence, in different combinations and at varying distances in a pre-selected gene desert of the human genome. As such, the researchers were able to create and study many different regulatory DNA landscapes. They discovered that only when the enhancer is located at a large distance from the gene, it required cohesin to activate gene transcription. They showed the enhancer itself recruits cohesin, and thus stimulates the local formation of DNA loops, thereby bringing the gene more often in its vicinity. These findings shed important new light on the functioning of enhancers, explaining much better how they can activate transcription of genes that are far away on the chromosome, and thus how different cells can use different genes to adopt different shapes and functions.

Expression of the gene (ā€˜Pā€™) in normal (control) cells (blue) and in cells lacking cohesin (purple), in six different regulatory DNA landscapes. From top to bottom, these regulatory DNA landscapes have the gene without an enhancer (noE), or with an enhancer (E) at increasing distances (0-11-47-100-407 Kb distances). The results (compare purple to blue) show that without cohesin gene expression goes up if the enhancer is at close distances (0-11 Kb), but down if the enhancer is at large distances (47-100-407 Kb). Thus, an enhancer needs cohesin to activate expression of distant genes.

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes. Niels J. Rinzema, Konstantinos Sofiadis, Sjoerd J. D. Tjalsma, Marjon J.A.M. Verstegen, Yuva Oz, Christian Valdes-Quezada, Anna-Karina Felder, Teodora Filipovska, Stefan van der Elst, Zaria de Andrade dos Ramos, Ruiqi Han, Peter H.L. Krijger, Wouter de Laat. Nature Structural & Molecular Biology, 2022.

Afbeelding Wouter de Laat



Wouter de Laat is group leader at the Hubrecht Institute, professor of Biomedical Genomics at the UMC Utrecht and Oncode Investigator.