“Too few” and “too fleeting”—these complaints are common among scientists who try to observe how genes are switched on and off when stem cells differentiate. These events, epigenetic maskings and unmaskings of DNA’s regulatory regions, take cells from the pluripotent state and to a particular cellular identity, a particular function. But even in a well-defined model of differentiation—hematopoiesis— chromatin state dynamics are elusive.
Current techniques require the sampling of millions of cells to reveal the epigenetic states through which cells pass when they leave the pluripotent state and mature into various kinds of blood cells. The number of blood stem cells is nowhere near this amount. Compounding this difficulty is the fact that each stage of development is exceedingly brief.
Now, however, scientists based at the Weizmann Institute and the Hebrew University of Jerusalem report that they have developed an epigenetic profiling technique that overcomes old technical limitations. With their approach, say the scientists, just a handful of cells—as few as 500—can be sampled and analyzed accurately.
“Using this powerful approach, we were able to identify the exact DNA regulatory sequences, as well as the various regulatory proteins that are involved in controlling stem cell fate—casting light on previously unseen parts of the basic program of life,” said Hebrew University’s Nir Friedman.
The scientists detailed their work in an article entitled, “Chromatin state dynamics during blood formation,” which appeared online August 7 in the journal Science. Here, the scientists described how they developed a high-sensitivity, indexing-first chromatin immunoprecipitation approach (iChIP) to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation.
“We identify 48,415 enhancer regions and characterize their dynamics,” wrote the authors. “We find that lineage commitment involves de novo establishment of 17,035 lineage-specific enhancers.”
The scientists determined that as many as 50% of these regulatory sequences are established and opened during intermediate stages of cell development, a result that suggests epigenetics is active at stages in which it had been thought that cell destiny was already set. “This changes our whole understanding of the process of blood stem cell fate decisions,” explained Weizmann’s David Lara-Astiaso. “[It appears] that the process is more dynamic and flexible than previously thought, giving the cell slightly more leeway at the later stages in deciding what type of cell to turn into, in case its circumstances change.”
In their conclusions, the researchers raised the possibility that development could involve massive dynamic reorganization of the chromatin landscape, pointing to a new model for chromatin dynamics during differentiation.
“We believe that the establishment of newly poised enhancers in the early lineage commitment steps initiates regulatory programs that are subsequently applied in differentiated cells, while closing of enhancers occurs during later differentiation stages,” the authors wrote. “This suggests that cellular enhancer potential reaches its maximum not at the hematopoietic stem cell stage but during the oligopotent progenitor stages.”
Although this research was conducted on mouse blood stem cells, the scientists believe that the mechanism may hold true for other types of cells. Discovering the exact regulatory DNA sequence controlling stem cell fate, as well as understanding its mechanism, hold promise for the future development of diagnostic tools, personalized medicine, potential therapeutic and nutritional interventions, and perhaps even regenerative medicine, in which committed cells could be reprogrammed and restored back to their full stem cell potential.