Researchers discover universal molecular 'flag' that highlights critical genes

Aug 01, 2014 by Bruce Goldman

After probing more than 200 genetic data sets, researchers at the Stanford University School of Medicine have identified a molecular flag that labels genes critical to a cell's function.

The flag appears to exist universally—in cells ranging from worms to humans—and can be used to help decipher the function of unfamiliar cells, said Anne Brunet, PhD, associate professor of genetics and senior author of the study. For example, by examining a cell's collection of flagged genes, researchers can classify a cell as a muscle, skin or other type of cell.

"This is the new era of using available data to make really new hypotheses and new discoveries," Brunet said. "This paper exemplifies why it's nice to be at Stanford where we're embracing big data."

The study was published in the July 31 issue of Cell.

This identifying flag is a long molecule, abbreviated as H3K4me3, that attaches to the proteins associated with DNA called histones. Other researchers had spotted this flag, but no one had probed its prevalence or significance. It generally marks about 1,000 genes in each cell, but the genes flagged vary among types of cells, Brunet said.

The molecule does not cue the cells to make more of the proteins encoded by the genes it marks. Instead, Brunet said, she believes it regulates how frequently the DNA is transcribed, ensuring that the critical proteins are produced methodically, like clockwork, rather than in spurts of rapid transcription followed by transcription-free gaps.

Uncharted territory

"I think the notion of transcriptional consistency is new, and it's very important," Brunet said. "This is completely uncharted territory."

Brunet and her team searched computerized data sets for the flag and genes associated with it in a variety of cell types and species and built a new database available for other researchers— bddb.stanford.edu —to examine the flag's association with genes in a variety of cells.

The researchers also mapped the flagged genes in mouse neural stem cells, the regenerative cells of the adult brain. The flag identified previously recognized genes that were critical, but it also marked several less well-understood genes, Brunet said. Researchers could also work backwards, using the flagged genes with known functions to figure out the cell type.

Uncharted territory

"I think the notion of transcriptional consistency is new, and it's very important," Brunet said. "This is completely uncharted territory."

Brunet and her team searched computerized data sets for the flag and genes associated with it in a variety of and species and built a new database available for other researchers—http://bddb.stanford.edu—to examine the flag's association with genes in a variety of cells.

The researchers also mapped the flagged genes in mouse , the regenerative of the . The flag identified previously recognized genes that were critical, but it also marked several less well-understood genes, Brunet said. Researchers could also work backwards, using the flagged with known functions to figure out the cell type.

The lead authors of the study are postdoctoral scholar Bérénice Benayoun, PhD; graduate student Elizabeth Pollina; and Duygu Ucar, PhD, a former postdoctoral scholar who is now an assistant professor at The Jackson Laboratory for Genomic Medicine in Connecticut.

In the future, Brunet said, her team plans to examine the molecular 's role in maintaining a cell's identity when faced by environmental changes, as well as its role in aging.

Explore further: Discovery may make it easier to develop life-saving stem cells

Related Stories

Scientists find new clues to brain's wiring

Jul 18, 2014

New research provides an intriguing glimpse into the processes that establish connections between nerve cells in the brain. These connections, or synapses, allow nerve cells to transmit and process information involved in ...

Recommended for you

Study on pesticides in lab rat feed causes a stir

Jul 02, 2015

French scientists published evidence Thursday of pesticide contamination of lab rat feed which they said discredited historic toxicity studies, though commentators questioned the analysis.

International consortium to study plant fertility evolution

Jul 02, 2015

Mark Johnson, associate professor of biology, has joined a consortium of seven other researchers in four European countries to develop the fullest understanding yet of how fertilization evolved in flowering plants. The research, ...

Making the biofuels process safer for microbes

Jul 02, 2015

A team of investigators at the University of Wisconsin-Madison and Michigan State University have created a process for making the work environment less toxic—literally—for the organisms that do the heavy ...

Why GM food is so hard to sell to a wary public

Jul 02, 2015

Whether commanding the attention of rock star Neil Young or apparently being supported by the former head of Greenpeace, genetically modified food is almost always in the news – and often in a negative ...

The hidden treasure in RNA-seq

Jul 01, 2015

Michael Stadler and his team at the Friedrich Miescher institute for Biomedical Research (FMI) have developed a novel computational approach to analyze RNA-seq data. By comparing intronic and exonic RNA reads, ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.