There are a couple cool stem cell papers in this month’s Cell.
Using a screen of chromatin regulating proteins in embryonic stem cells, UCSF’s Barbara Panning discovers something surprising. (See below)
Also see another cool article by Amy Wagers at Harvard, where her team was able to identify skeletal stem cells from look-alike cells and then show that these stem cells could rescue the phenotype of a mouse model of muscular dystrophy. It was written up in the Washington Post. and ScienceNews.
Packaging DNA for pluripotency
An RNA interference screen reveals a surprising player
Those picking the lock of pluripotency tend to focus on transcription factors. A combination of Nanog, Sox2, Oct4 and others allows cells to proliferate without differentiating. More recently, researchers have found that pluripotency depends not only on how transcription factors bind DNA, but also on how DNA is packaged up into chromatin.
To explore this function, researchers led by Barbara Panning at the University of California, San Francisco studied over 1,000 genes associated with chromatin regulation. Using RNA interference, they knocked out the genes one by one to see how that would change mouse embryonic stem (ES) cells. Sixty-eight genes affected the cells’ appearance or growth; 7 of these were part of a huge 17-member protein conglomerate called the Tip60-p400 histone acetyltransferase and nucleosome remodelling complex, and that’s where Panning decided to focus her efforts1.
“We knew it was going to be interesting because of the unusual change in the appearance and because it didn’t alter expression of the known pluripotency transcription factors,” says Panning. “It’s like we hamstrung the transcription factors.” Even though these factors were present in the cells, the cells didn’t look like typical ES cells: rather than growing in dense spheres, these cells grew in a flat layer with little cell-cell contact. They also couldn’t form teratomas or embryoid bodies.
Tip60-p400 is an unusual suspect; the protein complex is expressed in nearly all cell types and performs a range of housekeeping functions like DNA repair. It was not expected to have a special role in embryonic stem cells. But further work showed that although the complex generally has an activating role in normal cells, it has a repressive role in ES cells.
The team used chromatin immunoprecipitation to learn where in the genome the complex binds, and they found that it likely binds to the regulatory regions of most genes — in particular those regulatory regions that have been chemically marked with a chromatin modification known as H3K4me3. This mark is often found near that trigger differentiation and that are repressed in a sort of spring-loaded fashion. Proteins known as polycomb factors sit on these genes, physically blocking their expression in a way that can be quickly reversed.
But Panning suspects another mechanism is at work as well: many of the genes that are misregulated in the absence of Tip60-p400 are also misregulated in the absence of Nanog. However, the two do not seem to interact directly. Plus, she believes, the ten protein components of Tip60-p400 that weren’t identified in the initial screen have an interesting story to tell.
But there are also plenty of stories in those genes that were identified in the screen, says Rick Young, who studies ES cells and gene regulation at the Whitehead Institute in Cambridge, Massachusetts. He calls the publication a landmark study. “With this broad range of genes she’s identified, this protein complex is just the tip of the iceberg.”