Possible molecular mechanism for controlling DNA loop formation

Protein and DNA complexes within the cell behave like true nanomachines. We already know a lot about how some of them work, but in others we are only just beginning to get a general idea of ​​how they behave. The cohesin complex is one of the latter, formed by a group of proteins that are key in the processes of transcription and DNA replication. These proteins are particularly relevant in different types of cancer and in the context of rare diseases, such as Cornelia de Lange Syndrome, a genetic disorder that causes growth retardation, facial dysmorphism and limb defects, among other symptoms.

What is known so far is that the function of the cohesin complex is to generate, in a controlled manner, large DNA loops. But little is known about its control mechanisms.

Using computational simulation tools, the Molecular Modelling group at the Centro de Biología Molecular Severo Ochoa (CBM), part of the Consejo Superior de Investigaciones Científicas (CSIC) and the Universidad Autónoma de Madrid (UAM), in Spain, has proposed for the first time, as a control system for the described process, a ratchet mechanism, involving the proteins STAG2 and RAD21. This mechanism allows the unidirectional elongation of DNA loops, while blocking the recoil and, therefore, the shortening of these loops.

In recent years, leading research groups around the world have proposed several mechanisms to explain how DNA loops are formed from the structure of the cohesin complex. “Some have proposed caterpillar-type mechanisms, in which proteins advance on the DNA like a caterpillar on a branch. Others propose pumping mechanisms, similar to those of a caterpillar, but without the complex’s crawling motion. Regardless of the type of advance, all of these models would require a system that would prevent the protein complex from sliding backwards once it has pushed the DNA forward,” explain CBM researchers David Ros-Pardo, Íñigo Marcos-Alcalde and Paulino Gómez-Puertas. However, to date, no component of the system with a locking mechanism function, capable of providing directionality to the process, has been proposed.

This is the main novelty of the recent study, which proposes a role for two of the proteins in the complex, STAG2 and RAD21, which would act as a safety system capable of allowing the loop to advance, but not to retreat. “This system would work like a ratchet mechanism, similar to the tab on a plastic cable tie, which allows the loop to advance, but only in one direction,” the researchers add. The STAG2/RAD21 combination would allow the unidirectional sliding of the DNA, thus facilitating the extension of the loops and preventing their collapse.

Ratchet mechanism: STAG2/RAD21 complex blocking rightward movement on a DNA strand. (Image: Paulino Gómez Puertas)

Computational techniques for studying DNA

To carry out this study, computational techniques for dynamic molecular modelling were used, both at the atomic scale and at slightly larger scales, known as “coarse-grained” simulations. These types of approaches allow simulation times of several microseconds in complex systems, that is, systems containing several proteins moving along DNA strands of more than a hundred base pairs in length. All of this has been achieved thanks to high-performance computing systems, such as those housed at the Scientific Computing Centre of the Autonomous University of Madrid, integrated into the Spanish Supercomputing Network.

This study allows us, for the first time, to understand the regulation of DNA loop formation, a key mechanism in cellular processes such as gene expression or cell division. “Very importantly, it offers a mechanistic view of blocking DNA slippage and makes STAG2 and RAD21 proteins new potential targets in drug development,” explain the CBM scientists. These drugs could be able to stop or regulate cell division as future anti-cancer treatments or as possible treatments against Cornelia de Lange Syndrome and other related rare diseases.

The study is titled “STAG2-RAD21 Complex: a Unidirectional DNA Ratchet Mechanism in Loop Extrusion.” It has been published in the academic journal International Journal of Biological Macromolecules. (Source: CBM / CSIC / UAM)