Embryonic stem cells and induced pluripotent stem cells have a characteristic known as “pluripotency,” which simply means that they can become any cell type found in the adult human body. When these cells are given the proper cues, they can differentiate into muscle, skin, heart, blood, brain, or kidney cells, just to name a few. How do they do this?
A new study from the laboratory of Ali Shilatifard a scientist at the Stowers Institute for Medical Research in Kansas City, Mo, has shown that the plasticity of pluripotent stem cells partially comes from the stationing of a protein called EII3 at various stretches of DNA in the genome of these cells.
The vast majority of the cells in our bodies have a nucleus that houses the chromosomes, which are made of DNA. The DNA contains stretches known as genes that encode RNAs that are either translated into protein or have some other function. DNA stores genetic information and this genetic information is accessed by a complex set of enzymes called RNA polymerases and make these RNA molecules.
How do cells know when are where to make these RNA molecules? The signals for when to make a gene resides in sequences in or near the gene called “enhancer” sequences. Enhancers bind particular proteins and the assembly of particular proteins on the enhancers of a gene activate the expression of that gene.
EII3 is a member of a family of proteins known as the EII or (get ready) the “eleven-nineteen-lysine-rich-leukemia gene” (told you) family of elongation factors. ELongation factors increase the rate at which genes are expressed, and in pluripotent stem cells, EII3 parks itself at the enhancers of a variety of developmentally regulated genes, even ones that are silent in pluripotent cells.
According to Shilatifard: “We now know that some enhancer misregulation is involved in the pathogenesis of solid and hematological (that means blood-based) malignancies. But a problem in the field has been how to identify inactive or poised enhancer elements. Our discovery that EII3 interacts with enhancers in ES cells gives us a hand-hold to identify and to study them.”
EII3 was initially thought to be a dud because it was expressed at high levels in testes, which is a notoriously uninteresting tissue to work on from a gene expression perspective. All that changed when a postdoctoral research fellow in Shilatifard’s lab named Chengqi Lin searched all the potential places in the genome that EII3 could potentially bind in mouse embryonic stem cells. For this study, Lin collaborated with Alesander Garruss, another postdoctoral fellow in the Shilatifard lab, who is a specialist in bioinformational technologies. Lin and Garruss showed that EII3 occupies more than 5,000 enhancers, and many of these are affiliated with genes that regulate stem cell differentiation into spinal cord tissues, kidney cell types, blood cells and so on.
Lin put it this way: “What was interesting was that EII3 marked enhancers that are active and inactive, as well as enhancers that are known as “poised.” That indicated that EII3’s major function might be to prime activation of genes that are just about to be expressed during development.”
The fact that EII3 could prime silent genes for immediate expression under the right conditions was not a surprise, since researchers knew that enzymatic machine that copies DNA into RNA – RNA polymerase II, also known as Pol II, often pauses at the start of some genes. Pol II acts very like like a race car that has started its engine and is revving the engine in anticipation of the green light. When researchers in Shilatifard’s lab removed EII3 from the stem cells by means of a genetic trick, they discovered that the paused Pol II molecules disappeared these genes. This shows that EII3 oreferentiually marks stem cells enhancers and its presence there is necessary to keep an idling Pol II molecule there ready for action.
When the conditions are right, the EII3-Pol II complex interacts with the “Super Elongation Complex to give Pol II the green light and transcribe the gene. Without EII3, these genes are never expressed, even under the right conditions.
As a layer of icing on this remarkable research cake, Fengli Guo at the Stowers Institute use electron microscopy to prepare highly magnified images of mouse sperm DNA with Pol II and EII3 bound to this DNA. The significance of this come from development. Once fertilization occurs, the zygotes begins to divide, and the daughter cells are gradually committed to various developmental possibilities. The fact that EII3 is necessary for differentiation and that it is carried into the embryo by the sperm explains how the blastomeres of the early embryo are so exquisitely poised to readily differentiate into the various cell types that they eventually become.
“It is very significant that EII3 and other factors that regulate transcription are found in sperm,” said Lin. He continued to note that that it “would be exciting to further investigate whether transcription factors found in sperm could contribute to the decondensation of sperm chromatin or even further gene activation after fertilization by serving as epigenetic markers.”
Shilatifard is cautious about not overinterpreting these results, but he does think that they have fundamental implications for development and also, perhaps, cancer research. “This work has opened up a whole new area of research in my lab,” said Shilatifard, who has in the last decade focused on aberrant gene expression associated with leukemia. “If we find that transcription factors bind to specific regions of chromatin in germ cells, I may focus on germ cells in the next few decades. This would open a huge door enabling us to determine the role of these factors in early development.”