An international team of researchers from the Hubrecht Institute (KNAW) based in the Netherlands alongside those from the Max Planck Institute in Münster, Germany, has disproved the role of an essential protein, known as Oct4, in regulating gene expression.
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The research that was published this month in the Biophysical Journal explains how the protein was uncovered as activating genomic DNA, helping to open up the chromatin to facilitate gene expression.
Oct4 implicated in stem cell generation
DNA contains the blueprint for how each individual cell in the body is formed, it determines the type of cell it will be and what characteristics it will demonstrate.
This identity of the cell is dictated by which segment of the DNA is “read”, which is controlled by proteins within the cell called transcription factors that signal to a cell where to start and stop reading the DNA.
The identity of a cell changes as part of a natural transition from an undesignated cell, into a specific type of cell. Back in 2012, a team of Japanese researchers won the Nobel prize for their work which demonstrated that these transitions could also be reversed.
This work opened the door for new approaches to engineered cell types. This is important because people suffering from numerous diseases, such as Alzheimer's and Parkinson’s, may benefit from received these engineered cells. However, there is a need for the production of engineered cells to be more efficient.
The researchers involved in the current study recognized that there was a need to elucidate the exact mechanisms on a molecular level that are involved in converting cells back into stem cells.
In addition, previous studies had already revealed that Oct4, a particular transcription factor, is known to play a vital role in stem cell generation and along with 3 other pioneer factors it transforms adult cells into stem cells.
This previous research gave the team a candidate protein to investigate within its role in cell conversation.
World-first use of computer modeling in demonstrating how a transcription factor regulates gene expression
The researchers designed an experiment in which they were able to observe Oct4 binding to DNA at the nucleosomes. The team modeled Oct4 in different configurations. They found that only one of the two domains that the molecule consists of is able to bind to the nucleosome at the specific location of the DNA sequence.
Using computer simulations to model the behavior, the team uncovered which configurations were stable and what were the dynamics of the nucleosome's influence on Oct4 binding. This was the first time computer modeling had been used in this way.
The study represents the very first-time computer simulations have been used to demonstrate how gene expression is activated through the binding of a pioneer transcription factor to a nucleosome to initiate the opening of the chromatin.
The future of regenerative medicine
The team’s computational approach was able to determine how Oct4 regulates gene expression by binding to nucleosomes and opening chromatin, allowing the DNA to be read. Researchers believe that this approach is adaptable to screen other proteins to reveal how they interact with nucleosomes.
Oct4, known for its role in stem cell generation, was shown to facilitate gene expression of proteins that have the impact of initiated sequences that reset adult cells, converting them back to stem cells.
The genes that require activation for the initiation of this sequence are tightly packed within the chromatin. Oct4, along with other factors, helps to open the chromatin to allow the DNA to be read, giving it status as a pioneer transcription factor.
This research uncovered the underlying mechanisms allowing Oct4 to convert adult cells back into stem cells.
Next, more research will need to be conducted to explore how the model that the team has established can be used to develop new and more effective production methods of stem cells and other types of cells required by the field of regenerative medicine.
This will help patients with various illnesses and injuries restore or establish normal function in damaged cells, tissues, or organs.
Esch, D., Vahokoski, J., Groves, M., Pogenberg, V., Cojocaru, V., vom Bruch, H., Han, D., Drexler, H., Araúzo-Bravo, M., Ng, C., Jauch, R., Wilmanns, M. and Schöler, H. (2013). A unique Oct4 interface is crucial for reprogramming to pluripotency. Nature Cell Biology, 15(3), pp.295-301. https://www.ncbi.nlm.nih.gov/pubmed/23376973?dopt=Abstract
Huertas, J., MacCarthy, C., Schöler, H. and Cojocaru, V. (2020). Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding. Biophysical Journal. https://www.cell.com/biophysj/fulltext/S0006-3495(20)30032-1
Soufi, A., Donahue, G. and Zaret, K. (2012). Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome. Cell, 151(5), pp.994-1004. https://www.ncbi.nlm.nih.gov/pubmed/23159369?dopt=Abstract