DNA, like a tightly wrapped thread around a spool, is packaged into nucleosomes by wrapping around histones. Researchers at St. Jude Children’s Research Hospital have been investigating how pioneer transcription factors, a type of transcription factor, gain access to DNA even when it is tightly wound. Their study, published in Nature, provides insights into how the epigenetic landscape influences the binding of transcription factors, which could have implications for developing therapeutics for cancer.
Transcription factors are essential for regulating gene expression, but nucleosome packaging of DNA can physically prevent their access to binding sites. However, pioneer transcription factors have the unique ability to bind to their target DNA regions even within compacted chromatin and facilitate the binding of other transcription factors.
One group of pioneer transcription factors, known as Yamanaka factors, includes Oct4, which is used to induce pluripotency. The mechanism by which pioneer transcription factors access tightly wound DNA has remained unclear. To shed light on this process, scientists at St. Jude employed cryo-electron microscopy (cryo-EM) and biochemistry techniques to investigate how Oct4 interacts with nucleosomes.
“Building on previous studies exploring the dynamic behavior of nucleosomes, we aimed to uncover how other factors exploit these dynamic changes to access chromatin,” explained Mario Halic, Ph.D., the corresponding author from St. Jude’s Department of Structural Biology. “Contrary to our expectations, Oct4 did not bind to the inside of the nucleosome but rather to a region slightly outside.”
One of the key findings of the study is that epigenetic modifications can influence the binding of transcription factors and their cooperative interactions. The preexisting epigenetic state of chromatin plays a crucial role in determining how transcription factors bind cooperatively to chromatin.
In summary, this research provides a deeper understanding of how pioneer transcription factors access tightly wound DNA and how the epigenetic landscape affects transcription factor binding. These findings may contribute to the development of future therapeutic approaches targeting transcriptional dysregulation in cancer and other diseases.
The epigenetic impact
The study’s results demonstrate that the initial binding of Oct4 to the nucleosome induces a structural change that exposes additional binding sites. This phenomenon promotes the binding of other transcription factors, elucidating the concept of transcription factor cooperativity. The researchers also observed that Oct4 interacts with histones, and these interactions facilitate the opening of chromatin and influence cooperativity.
Furthermore, the study revealed that modifications at histone H3K27 impact the positioning of DNA by Oct4. These findings provide an explanation for how the epigenetic landscape can regulate Oct4’s activity, ensuring proper cell programming.
An interesting aspect of the research is that the scientists utilized endogenous human DNA sequences rather than artificial ones to assemble their nucleosomes. Although more challenging, this approach allowed them to investigate the dynamic nature of the nucleosome.
“We chose to employ authentic genomic DNA sequences to examine the behavior of transcription factors within their functional context,” explained Kalyan Sinha, Ph.D., the first author from St. Jude’s Department of Structural Biology.
“Our approach enabled us to discover that the initial binding event of Oct4 positions the nucleosomal DNA in a manner that facilitates the cooperative binding of additional Oct4 molecules to internal sites. Additionally, we observed intriguing interactions with histone tails and observed that modifications to histones can influence these interactions. Together, these findings offer fresh insights into the pioneering activity of Oct4.”
Sinha further emphasized, “Histone modifications influence the positioning of DNA and the ability of transcription factors to bind cooperatively. Therefore, within cells, the same DNA sequence can yield different combinatorial effects on transcription factor binding due to distinct epigenetic modifications.”