Whitehead Scientists Discover Critical Role Played By One Enzyme In Embryonic Stem Cell Differentiation

Cells use gene expression programs to respond to external stimuli and maintain their present form and identity. Genes are stretches of DNA that encode a protein or RNA. Gene expression requires DNA sequences directly attached to the gene, and these sequences are called the “promoter” of the gene. The promoter is the binding site for the enzyme that executes the first step of gene expression. That enzyme is called “RNA polymerase.” RNA polymerase binds to the promoter and initiates the synthesis of an RNA copy of the gene, and process by which an RNA copy of the gene is synthesized rom the DNA template is called “Transcription.”

If the gene encodes a protein, the RNA is processed and sent from the nucleus of the cell to the cytoplasm, where protein/RNA complexes called “ribosomes” use the sequence in the RNA to make proteins that have amino acid sequences. Some genes, however, encode RNA molecules that are not used to direct the synthesis of protein, but are used for some other purpose.

Whatever the case, cells have a great deal of DNA in their nuclei. Almost every human cell, for example, contains so much DNA that if the DNA in one human cell was laid out end-to-end, it would stretch to a length of at least 1 meter. To pack all that DNA into the nucleus of a cell, the DNA is wound into a tight complex of DNA and proteins that is collectively called “chromatin.” Chromatin consists of DNA wound around proteins called histones, in ways that resemble the way thread is wound around a spool. These little histone spools are then wound into spirals that are then wound into a rosette of fibers. It is exceedingly for RNA polymerase to transcribe genes when they are wound into chromatin. How then are genes expressed? It turns out that particular proteins modify chromatin and cause it to loosen up so that RNA polymerase can access it.

Histone modifying proteins include those that encourage the formation of chromatin and tend to shut gene expression off (histone deacetylase, Polycomb-group proteins), and those that loosen chromatin and encourage gene expression (histone acetyl-transferases, histone methyltransferases). Therefore, we might expect to see such enzymes playing an important role in stem cell differentiation.

Therefore, we should not be surprised that stem cells researchers at the Whitehead Institute have discovered that a specific chromatin enzyme called lysine-specific demethylase 1 (LSD1) plays as embryonic stem cells differentiate into other cell types. Cell differentiation requires two key steps: 1) the genes active in the initial cell type must be deactivated; and 2) those genes important for the establishment of the new cell type must be activated. If the switch is not flawless, a transitioning cell may die or be driven to divide uncontrollably. Interestingly, LSD1 was known to be critical to development, but little was known about the key role it plays during differentiation, when cell-specific gene expression systems are switched on or off.

Paper author, Steve Bilodeau, who is also a postdoctoral research fellow in the laboratory of Whitehead Member, Richard Young, said; “We knew that cells express a new set of genes when the operating switch occurs. But this study shows it is also essential to shut off genes that were active in the prior cell state. If you don’t, the new cell is corrupted.”

Bilodeau and Warren Whyte, a Young lab graduate student and co-author, redefined LSD1’s role and described a previously unknown mechanism for silencing genes. They examined embryonic stem cell gene expression during differentiation and concentrated their efforts on those genes that must be shut off during differentiation. Whyte and Bilodeau found LSD1 was located on the promoters of those genes that had to be repressed in order for differentiation to occur. LSD1 was also found near DNA sequences called “enhancers,” which are associated with promoters and increase the ability of the promoters to activate gene expression.

What is LDS doing at the promoter and enhancer? When LSD1 receives the signal that the stem cell is going to differentiate, it transitions into an active conformation and silences those genes. Specifically, LSD1 hamstrings the ability of the enhancers of those genes to activate gene expression. With their enhancers rendered nonfunctional, transcription of these genes is silenced. While this occurs, other mechanisms switch on those genes necessary for the adoption of the new cell type.

Whyte added: “This reveals the critical function of LSD1 in cell differentiation. The enzyme decommissions the stem cell enhancers, thus allowing the new cell to function entirely within the parameters of the new operating system.”

Although this work focuses on one enzyme’s job in normal cells, Young sees broader implications, since LSD1 is a member of a class of molecules that regulate both gene activity and chromosome structure. Therefore, these findings about LSD1 could provide insights into how related regulators function. Similarly, understanding how a mechanism operates in normal cells provides a solid foundation for teasing apart what is going wrong in abnormal cells.

Young summed it up this way: This new knowledge brings us one important step closer to understanding defective operating systems in diseases such as cancer. And this may give us a new angle on drug development for these diseases.”

This work was published in “Enhancer decommissioning by LSD1 during embryonic stem cell differentiation;” Warren A. Whyte, Steve Bilodeau et al.; Nature, 2012; DOI: 10.1038/nature10805.