Using a technology he invented, Brown researcher William Fairbrother (pictured center) and colleagues have discovered new molecular interactions in the process that will help regenerative medicine researchers better understand pluripotency.
In a study, Fairbrother's
team showed that different proteins called transcription factors compete and cooperate in the cells to produce complex bindings along crucial sequences of DNA.
This game of molecular "capture the flag," played in teams and amid shifting alliances, appears to be a necessary part of what determines whether stem cells retain their pluripotency and whether specialized, or differentiated, cells can regain it.
In recent years scientists have reported spectacular successes in turning fully differentiated cells back into pluripotent stem cells, a process called reprogramming.
But the animals derived from these cells often suffer higher rates of tumors and other problems, Fairbrother
The reason may be because the complex details of the reprogramming process haven't been fully understood.
said there are many misconceptions about how reprogramming transcription factors interact with DNA.
"Most people think of a protein binding to DNA as a single, surgical thing where you have this isolated binding event," Fairbrother
"But in fact we show that sometimes these binding events occur over hundreds of nucleotides so they seem more like great greasy globs of proteins that are forming.
In addition, the proteins interact with each other, diversifying their function by appearing in complexes with different partners at different places."
By employing a high-throughput, high-resolution binding assay that he's
dubbed MEGAShift, Fairbrother
colleagues, who include pathology researchers from the University of Utah School of Medicine
, were able to analyze the interactions of several key transcription factors in a region of 316,000 letters of DNA with a resolution as low as 10 base pairs.
Through hundreds of thousands of array measurements, lead authors Luciana Ferraris (pictured left) and Allan Stewart, Fairbrother
, Alec DeSimone (pictured right), and the other authors learned of previously unspotted patterns of protein interactions.
"Who binds next to a protein is a determinant of who ends up binding to a sequence," Fairbrother
With support from the National Institutes of Health
group is also applying MEGAShift to other questions, including how protein-protein interactions affect the formation of RNA-protein complexes, which can be even more complicated than binding DNA.