New insights into how genes are activated

In a study in Nature, researchers at Karolinska Institutet present a new method for analysing how instructions in the genome control how our genes are activated in individual cells. The results give new insights into how the genome encodes for its own use, which increases our basic understanding of how genes are activated in different types of cell in the body in both good and ill health.

Almost all cells in the body have the same set of DNA and can in principle become any kind of cell at all. What distinguishes the cells is the way in which the genes in our DNA are used.

All the DNA in a cell is called the genome, our genetic material, but only a very small part of a human’s genome consists of genes. Instead extensive areas of the genome are used to regulate when and in which cells nearby genes are active. These regions contain “enhancers” and the gene sequences located right next to the genes, “promoters”. In a diseased body, these regions are often mutated and a deeper understanding of the function of these regions would bring light to the course of the disease in question.

In order for a gene to be used, it must be translated from DNA to copies of RNA. RNA is similar to DNA but its structure is slightly different and it can be used as a template for producing protein. The translation of DNA to RNA is called transcription.

Method to sequence RNA in individual cells

There are still many things that are not clearly understood about how transcription takes place and how it is regulated. For example, if a gene is used by a cell, the gene’s DNA is not translated to RNA all the time. That would require too much energy. Instead, the transcription takes places in bursts, when the transcription machinery is recruited and several RNA molecules are produced in a short time. The transcription of each gene can be characterised on the basis of the kinetics of this process, that is, the frequency of the bursts and the number of molecules produced during the bursts.

”It used to be difficult to measure the kinetics and how many RNA molecules had been produced by a gene in an individual cell. The methods that have existed up to now were only able to follow a few genes at a time. Moreover, mammals have two sets of almost all their genes so it has been difficult to distinguish between the RNA that comes from the mother’s version of the gene and that from the father’s version,” says Rickard Sandberg, professor at the Department of Cell and Molecular Biology at Karolinska Institutet, who has led the study in question.

In the study, the researchers used a method which they had developed themselves to sequence RNA in individual cells. The method makes it possible to measure the number of RNA molecules for almost all the genes used in a cell.

Variation found in the genes of two different types of mouse

The researchers sequenced cells of connective tissue and embryonal stem cells from a crossbreed of two distantly related mice. With the help of the natural variation found in the genes of the two different types of mouse, the researchers were able to distinguish between the sequenced RNA from the mother’s and the father’s versions of the gene and in that way measure the transcription exactly. They then used a mathematical model to make estimations, for each of the versions, of how often the gene is transcribed and how much RNA is then produced.

”We discovered that enhancers did affect how often a gene was transcribed in the two different cell types but not how many RNA molecules were produced. We also found that certain DNA sequences located at the beginning of a gene can influence how much RNA is produced in a burst. In that way, we have begun to chart how the genome encodes for its own use,” says Anton Larsson, the first author of the study in question and a doctoral student in Rickard Sandberg’s research group.

”It will be possible to make wide use of our method to chart at a much deeper level how different proteins affect the transcription process,” says Rickard Sandberg.

The research was funded with support from the European Research Council, the Swedish Research Council, the Knut and Alice Wallenberg Foundation and the Vallee Foundation.

Publication

“Genomic encoding of transcriptional burst kinetics”
Anton Larsson, Per Johnsson, Michael Hagemann-Jensen, Leonard Hartmanis, Omid R. Faridani, Björn Reinius, Åsa Segerstolpe, Chloe M. Rivera, Bing Ren and Rickard Sandberg.
Nature, online 2 January 2018.