The fate of an embryonic stem cell, which has the potential to become any type of body cell, is determined by a complex interaction of genes, proteins that bind DNA, and molecules that modify those genes and proteins.

In a new paper, biologists from MIT and the University of California at San Francisco have outlined how those interactions direct the development of stem cells into mature heart cells. The study, the first to follow heart-cell differentiation over time in such detail, could help scientists better understand how particular mutations can lead to congenital heart defects. It could also assist efforts to engineer artificial heart tissue.

"We're hoping that some of the information we've been able to glean from our study will help us to approach a new understanding of heart development, and also lead to the possibility of using cells that are generated in a dish to replace heart cells that are lost as a consequence of aging and disease," says Laurie Boyer, an associate professor of biology at MIT and a senior author of the paper, which appears in the Sept. 13 online edition of Cell.

Research in Boyer's lab focuses on how DNA is organized and controlled in different cell types to create the wide variety of cells that make up the human body.

Inside a cell, DNA is wrapped around proteins called histones, which help control which genes are accessible at any given time. Histones may be tagged with different chemical modifications, which influence whether a particular stretch of DNA is exposed or hidden.

"These modifications cause structural changes that can act as docking sites for other factors to bind," says Joe Wamstad, a postdoc in Boyer's lab and one of the lead authors of the Cell paper. "It may make the DNA more or less accessible to manipulation by other factors, helping to ensure that you don't express a gene at the wrong time."

In this paper, the researchers found that histone-modification patterns shift rapidly as a stem cell differentiates. Furthermore, the patterns reveal genes that are active at different stages, as well as regulatory elements that control those genes.

Tracking development

To discover those patterns, the researchers grew mouse embryonic stem cells in a lab dish and treated them with proteins and growth factors that drive heart cell development. The cells could be followed through four distinct stages, from embryonic stem cells to fully differentiated cardiomyocytes (the cells that compose heart muscle). At each stage, the researchers used high-throughput sequencing technology to analyze histone modifications and determine which genes were being expressed.

"It's basically watching differentiation over time in a dish, and being able to take snapshots of that and put it all together to try to understand how the complex process of cardiac commitment is regulated," Boyer says.

The researchers found that they could identify groups of genes with related functions by comparing their modification patterns and whether they were being transcribed at a particular time. They also identified regulatory regions located far away from the genes they regulate. Many of these regions were located in sections of DNA previously thought to be "junk." Recent studies have revealed that much of this DNA actually plays important roles in regulating gene expression.

"We're starting to link genes with the regulatory elements that may be activating them, and beginning to draw a picture of the molecular circuitry that is controlling and driving these cardiac-specific programs -- the DNA elements that are important for turning on all the genes that you need to make a heart cell," Wamstad says.

The team also identified transcription factors -- proteins that initiate the expression of genes -- that appear to work collaboratively at regulatory regions to drive transcription of genes important for cardiac development. Defects in many of these transcription factors have previously been linked to congenital heart defects.

Linking disease with DNA

Previous genome-wide sequencing studies have revealed genetic variations that are more common in people with congenital heart disease or cardiovascular disease. The data obtained in this study should help researchers figure out why those variations give rise to such diseases.

The findings could also help researchers figure out how to create heart cells for possible therapeutic use, says Richard Lee, a professor of medicine at Harvard Medical School and member of the Harvard Stem Cell Institute.

"It's a roadmap of how the heart cell develops, and it's a tremendous achievement," says Lee, who was not part of the research team. "The work shows that the heart cell develops through coordinated gene expression transitions, and how those transitions are controlled. This study will help us to understand how to make new heart cells, which has been a big challenge for treating heart failure."

The researchers are now looking for other combinations of transcription factors that are involved in controlling cardiac differentiation. They are also studying variations in the regulatory sequences they identified to figure out how these sequences might give rise to congenital heart disease or susceptibility to cardiovascular disease later in life.

The research was funded by the National Heart, Lung and Blood Institute; the National Institutes of Health; the Lawrence J. and Florence A. DeGeorge Charitable Trust; the Massachusetts Life Sciences Center; and the Pew Scholars Program in the Biomedical Sciences.