Control, form and purpose

To which sites on messenger RNA will certain microRNA molecules bind? The institute's scientists offer a surprising answer

The human genetic load contains about 20,000 to 30,000 genes, which, according to the information encoded in them, produce different proteins. This process, called "gene expression", is controlled by complex and branched mechanisms, which determine which of the genes will be expressed, in which cell, when, and to what extent. The proteins that are formed at the end of this process determine how the living cell will function, which affects the entire organism. Thus, for example, gene expression is a central element in embryonic development. In the adult organism, it affects processes such as the formation of blood vessels, metabolism, and also the development of various diseases, including cancer. microRNA molecules are one of the control factors that affect the process of protein production in the body at a relatively late stage: the stage where a messenger RNA molecule (which was created according to the information in the gene that other control factors have already "triggered" ), makes its way towards the ribosomes, the protein factories of the cell. The microRNA molecule binds to a specific target site on the messenger RNA molecule, thereby preventing the production of the protein it codes for. To date, hundreds of different types of microRNA molecules have been identified, with each microRNA having a different set of target genes. To understand this process, one must find the target sites, on messenger RNA, to which the microRNA molecules bind. Identifying these target sites may also help in understanding the disruptions that cause the uncontrolled expression of genes, a process that causes certain diseases.

To find the target sites, many scientists focus on identifying chemical matches between the sequence of different segments in the two molecules (similar to the match that exists between the two helices of the DNA molecule). But in fact, in many cases, there is no perfect match between the microRNA base sequence and the base sequence at the target site. Scientists who wanted to understand this phenomenon developed methods for predicting the target sites, which look for a partial match between the sequence of the microRNA bases and the sequence of the bases in the target site. However, the requirement for partial matching leads to many target site predictions that have been experimentally proven to be incorrect. In an attempt to improve the predictive ability, the methods got more and more complicated, but in the end they failed to fully and accurately predict to which sites on the messenger RNA certain microRNA molecules would bind.

Dr. Eran Segal and research student Michael Kerts, from the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, chose to investigate the process from a different direction: instead of examining the chemical sequence of the molecules, they focused on the spatial, three-dimensional structure of the RNA molecule -delivery person. Together with a group of researchers from Rockefeller University in New York, they tested whether folds in messenger RNA affect the binding of microRNA molecules to their target sites. The scientists created mutations that caused the messenger RNA to fold and close the target sites, or, on the contrary, to open and expose them. Then compare the expression level of the original gene to that of the gene with the mutations. "According to the existing theories, these changes should not affect the expression of the gene, since the mutations were not carried out in the bases involved in the direct contact between the molecules, but in the bases adjacent to them," says Dr. Segal. The results of the experiments showed unequivocally that the spatial structure of the target site in the messenger RNA molecule does affect the level of gene expression. When the target site is in an open area and easy for the microRNA molecules to access, more microRNA molecules adhere to the messenger RNA, which causes a strong inhibition of the production of the protein whose construction information is carried by the - AN messenger. Conversely, when the target site is closed, there are fewer adhesions between the molecules - and gene expression increases dramatically.

The scientists developed a formula that explains the interactions between microRNA molecules and their target sites, and which allows new target sites to be identified. The formula consists of the difference between the energy that must be invested to open the target site (in the case of a closed structure a high investment will be needed, in the case of an open structure the investment will be negligible), and the energy emitted when the microRNA binds to the target site (in the case of a high match In the sequence of bases, a large amount of energy will be released, and in the case of a partial match, a smaller amount will be released). The higher the value obtained, the more likely it is to be a potential microRNA target site.

Another discovery that emerges from the research is that the binding of a microRNA molecule to messenger RNA does not depend only on the open structure of the target sequence itself, but also on that of the sequences adjacent to the target site. The reason for this is that the microRNA molecule is contained within a large protein structure, and the entire structure must be allowed easy access to the target site. Following this discovery, the researchers made an adjustment to the formula, so that the "energy investment" component includes the energy that must be invested to open the target site in a way that fits the entrance of the entire protein structure. This adjustment improved the accuracy and predictive ability of the model. Next, the researchers created four catalogs that define potential microRNA target sites across human, mouse, fly and worm genomes. An examination of all organisms showed that the target sites are in exposed, unfolded sites, which indicates that the spatial structure of messenger RNA, which determines the binding sites for microRNA, has played an important role throughout evolution. The results of the study, recently published in the journal Nature Genetics, provide scientists with a useful tool that allows them to scan genetic sequences and identify possible microRNA target sites based on both sequence and spatial structure.

Although it is a simple and reliable model, and a considerable improvement of the means that researchers had until now, the scientists point out that the calculations are not XNUMX percent accurate, also because it is difficult to accurately calculate the energetic cost of opening the target site, but mainly because the cell is not a sterile environment, and exist within it A host of factors also affect the binding of the microRNA to the target site. Research student Michael Kerts: "The beauty of this study is that, despite all the components and factors present in the cell, which we did not take into account, our simple model is still based solely on the interaction between the microRNA and the target site, and on the structure The secondary of the target site explains the experimental results quite well."