Transcription factors target tightly packed DNA to initiate reprogramming

16 April 2015

Tremendous advances in the field of stem cells have made it possible to convert cells into other types using transcription-factors-mediated reprogramming methods in the laboratory.

The open challenge is to transform this technology into an effective and safe method in the clinic. Revealing the intricate details, underpinning the reprogramming process, will help researchers find new ways to generate the quantity and quality of cells that are required for cell replacement therapy in situations such liver and heart diseases.

Prior to his recent move to the MRC Centre for Regenerative Medicine (CRM), group leader Abdenour Soufi worked at the Perelman School of Medicine at the University of Pennsylvania in the laboratory of Prof. Kenneth S. Zaret, director of the Institute for Regenerative Medicine.

Soufi and colleagues discovered how the reprogramming factors Oct4, Sox2, Klf4 and c-Myc bind and interact with tightly packed and normally inaccessible DNA. The results of their findings were published in the scientific journal Cell earlier today.

Zaret commented:

“We found that pioneer protein activity relates simply to the ability of a transcription factor to adapt to particular areas of DNA building blocks on the nucleosome surface. This was an ‘aha moment’ of simplicity”.

reprogramming blueprint
The pioneer transcription factors but not c-Myc bind to nucleosomal DNA c-Myc is too rigid, and the two “legs” of the TF would have to cover most of the DNA surface, leaving only a small fraction free to bind to histones (white arrow), which is incompatible with the nucleosome structure. The pioneer transcription factors, on the contrary, are much more flexible and are able to adapt to a much smaller fraction of the DNA, leaving the region that binds to histones free. This is compatible with the proposed mechanism in which these factors bind silenced DNA first and lay the foundations for other TFs to interact.

Zaret continued:

“We all want to know how to transform one cell into another. Now we understand how that happens at the first step. We are working on how the pioneer gene regulatory proteins physically open up the chromatin to loosen it, in preparation for gene activity. These points are fundamentally important for understanding tissue development, cell regeneration, and for making designer cells.”

CRM Dr. Abdenour Soufi added:

“The field is relying on “natural” transcription factors such as Oct4, Sox2, Klf4, and c-Myc to perform the “unnatural” task of reprogramming differentiated cells from one type to another. This is partly why cellular conversion is extremely inefficient and variable.”

“My work at CRM will now focus on creating a blueprint to engineer novel factors with improved reprogramming efficiency and fidelity.”

Notes to editors