Computer simulations depict how a basic stem cell protein unlocks coiled DNA

The original genomic nucleosomes are linked (dark blue) by 4 October (red) and in free form (yellow). DNA surfaces and bands show the basic structural regions of histones, respectively. Credit: Vlad Kojokaru

A key protein for converting adult stem cells into cells resembling embryonic stem cells has been imaged in unprecedented detail by an international team of researchers around Hans Schuler and Vlad Kojokaru of the Max Planck Institute for Molecular Biomedicine in Münster. By combining experiments with computer simulations, the team envisioned how the Oct4 protein binds to and opens up short pieces of DNA as it wraps around nuclear storage proteins (histones), just as it does in our genome. The results were published in the journal nucleic acid research On September 22.

grown ups cells They can be converted into embryonic stem cell-like cells (induced pluripotent cells, iPSCs) using a combination of only four proteins. In recent years, this cellular reprogramming technology has contributed significantly to disease modeling, drug development, and cell replacement therapies. However, many questions about the molecular mechanisms of this conversion remain unanswered. For example, one of the essential steps is to unlock the DNA in the cells to be transformed. Each of our cells contains about two meters of DNA packaged in a structure known as chromatin. In chromatin, DNA is tightly wrapped around histones in repeating structural units known as nucleosomes. So how do these four proteins unlock DNA when they are expressed in adult cells?

October 4: A leading regulator of pluripotent stem cells

Three of the four proteins have been described as pioneer transcription factors, meaning that they bind to specific DNA sequences as they are wrapped in nucleosomes and have the ability to open chromatin directly or indirectly. Among the three, October 4 stands out because it is essential for maintenance embryonic stem cells of different species and to reprogram human cells. October 4 was discovered in the late 1980s by Hans Schuler at about the same time as two other laboratories and is the only irreplaceable agent in the Nobel Prize winning Shinya Yamanaka cocktail for reprogramming adult cells into pluripotent cells. About 10 years ago, Abdelnour Sophie and Ken Zarett described regions of mobilized DNA that had been associated by 4 October in the early stages of reprogramming.

Caitlin MacCarthy, a postdoctoral researcher in Hans Schöler’s group and one of the study’s lead authors, provided the wet lab experiments. Reflecting on her work, McCarthy explains: “The experiments were more difficult than we expected. Working with genetic or original nucleosomes has become somewhat technical because they are very dynamic, unlike more stable geometric sequences. However, we were able to accurately show where October 4 is associated with them “. So what happens when Oct4 binds nucleosomes?

Computational nanoscope

To answer this, Jan Huertas, who is also the study’s lead author, presented his simulations during his PhD. Studies at MPI Munster. He and Vlad Kojokaru used computational nanoscopy to visualize how Oct4 binds to nucleosomes and affects their structure. Researchers use the term computational nanoscope to refer to a set of computer simulations that enable them to visualize the motions of molecules over time.

The accuracy of these methods is now so high that one can imagine observing molecules under a high-resolution microscope. Nucleosomes, like all molecular structures in our cells, are dynamic. They move, twist, breathe, unwrap, and roll again. Imagining these movements in experiments is often impossible. Huertas explains, “It’s so amazing to be able to watch these large molecular structures with all their atoms moving around on the computer and to know that what you’re seeing is so close to what’s actually going on.”

4 october opens nucleosomes

In the real-time films of the Oct4-nucleosome complexes they generated, each showing 1 to 3 microseconds of complex life, Huertas and Cojocaru observed how Oct4 is able to open nucleosomes. They describe in atomic detail the mechanisms of this opening by comparing the movements of free and bound nucleosomes to Oct4.

Interestingly, the opening depended on the position of the DNA sequence recognized by Oct 4 on nuclear and on the mobility of the terminal elastic regions of histones, known as histone tails.

Towards an understanding of the leading factors and transformations of cell fate

The researchers are excited about the implications of their work and their future perspective. “Here we show for the first time in atomic detail not only how Oct4 binds to different nucleosomes, but also how Oct4 binding affects the Histone tails on the structural flexibility of these nucleosomes.”

McCarthy adds that “because, like pioneer factors, histone tails are also major regulators of gene expression. While pioneer factors bind to DNA to open chromatin and activate genes, histone tails carry chemical modifications that define the open regions of chromatin from which genes can be expressed.”

Huertas further explains that, “Until now, it has been a mystery how histone tails affect the ability of pioneering factors to bind and open nucleosomes. Our work paves the way for future studies of other pioneering factors, many of which are key to cellular transformations, including cell fate transformations and cancer.”

Says Cojocaru, “The mechanism we describe here fills a knowledge gap in understanding how factors such as Oct4 induce cell-fate shifts. Understanding these mechanisms will ultimately provide means to improve and control these transformations for successful use in therapeutics.” computer simulation You will be at the center of these future discoveries.”


Computer simulations depict how DNA is recognized to turn cells into stem cells


more information:
Caitlin M MacCarthy et al, phosphorylates OCT4 and enhances the plasticity of the nucleus, nucleic acid research (2022). DOI: 10.1093/nar/gkac755

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