Using computer simulations, MIT chemists have discovered how molecules interact with chromosomes in the nucleus. Thanks to these interactions, the nuclei take the form of droplets. The interaction of chromatin with the nuclear body leads to the fact that the genome acquires a gel-like structure. This promotes stable interactions between genome and transcriptional mechanisms, which helps to control gene expression.

Gene expression is the process by which hereditary information from a gene is converted into a functional product – RNA or protein.

Scientists used molecular dynamics modeling method. With it, they modeled how a molecular system changes over time. At the beginning of the simulation, the proteins and RNA that make up the small nuclei are randomly distributed throughout the nucleus. Simulation tracked how they gradually form small droplets.

Ribonucleic acid (RNA) is one of the three main macromolecules (the other two are DNA and proteins) that are found in the cells of all living organisms and play an important role in the coding, reading, regulation, and expression of genes.

In the modeling, the researchers also included chromatin: a substance that makes up chromosomes and includes proteins. Using data from previous experiments that analyzed the structure of chromosomes, the team calculated the interaction energy of individual chromosomes, which allowed them to represent the 3D structure of the genome.

Using this model, the researchers observed how droplets of small nuclei were formed. They found that if they had modeled the components of the small nuclei inside the nucleus on their own, without chromatin, they would fuse into one large blob. Once chromatin was introduced into the model, the researchers found that the small nuclei formed many droplets.

Scientists have explained why this is happening. Small nuclei bind to specific regions of chromatin, chromatin acts as a brake that prevents small bodies from fusing with each other.

“The connection we see between chromatin and nuclear bodies is not specific to small nuclei. This also applies to other nuclear organs, scientists say. “This concentration of the nuclear body fundamentally changes the dynamics of genome organization and is likely to transform the genome from liquid to gel.”

The gel state will facilitate the interaction of different chromatin regions with each other much more than in a liquid structure. Maintaining stable interactions between distant regions of the genome is important because genes are often controlled by regions of chromatin that are physically distant from them.

The cell stores genetic material in the nucleus in the form of chromosomes. The nucleus is home to small bodies, clusters of proteins and RNA that help build ribosomes.

The ribosome is the most important non-membrane organelle of all living cells, which serves for the biosynthesis of protein from amino acids according to a given template based on genetic information provided by messenger RNA.