Linear array of chromosomes in a variety of structures and sizes. Image credit: Kate Whitley (CC BY 4.0)
Inside cells, genetic information is stored within molecules of DNA that are folded into three-dimensional structures known as chromosomes. Each fold in a chromosome forms when two points on a single DNA molecule link together to make a loop. DNA in two different chromosomes can also form links with each other (known as “contacts”). Many cells contain two copies of every chromosome and these copies are often able to make contacts with each other.
DNA loops and contacts can change in response to the environment and this may help cells switch the right genes on and off at specific times. For example, in budding yeast cells that have used up most of their preferred food source – a sugar called glucose – the two copies of a region of DNA known as the HAS1pr-TDA1pr region stick together. This may help the budding yeast cells switch on genes that are needed to make use of alternative sources of food.
Cells contain hundreds of proteins called transcription factors that can bind to specific locations on DNA and can also stick to each other. These proteins are thought to be responsible for anchoring bridges between the DNA at most loops and contacts. One way to find out which transcription factors form specific DNA loops and contacts is to generate many different genetic mutations in the DNA and identify precisely which mutations disrupt the links. However, current methods can only test one mutation at a time, so it remains unclear how and why many segments of DNA stick together.
Now, Kim et al. have developed a new method known as MAP-C to test how hundreds of mutations in budding yeast affect a particular DNA contact, in a single experiment. The MAP-C method was used to test which mutations within either the DNA segment involved in the contact, or in genes encoding transcription factors, prevent copies of the HAS1pr-TDA1pr region from forming contacts. This revealed that three transcription factors – Leu3, Sdd4, and Rgt1 – bridge contacts between the two copies of HAS1pr-TDA1pr.
Mutations that disrupt the three-dimensional structure of chromosomes can cause cancer, developmental disorders and other diseases. The MAP-C method will allow researchers to better understand which transcription factors control how DNA is folded inside the cell, and which mutations change this folding.
