Yale maps “uncharted” genome regions

Non-coding regions of the human genome play a larger role in cell function than previously thought, scientists from Yale and other schools have shown.
Non-coding regions of the human genome play a larger role in cell function than previously thought, scientists from Yale and other schools have shown. Photo by Jennifer Gersten.

Scientists from Yale and an international research consortium recently published the discovery of information identifying functional regions of the human genome.

Whereas the human genome, sequenced under the worldwide Human Genome Project in 2003, defines the overall structure of human DNA, the new project, titled Encode (ENCyclopedia Of DNA Elements), investigated how many of the elements of DNA work to control activity within the body. The results of Encode, published in over two dozen scientific journals, annotated the human genome by identifying regions previously considered “junk” as essential for determining cell function. Knowledge gained by the project will help scientists better understand the role of genes in human development and disease, said Sherman Weissman, professor of genetics at the Yale School of Medicine and a member of the project.

The Yale division of Encode was led by Michael Snyder, former chairman of the Yale Department of Molecular, Cellular and Developmental Biology, and launched worldwide in 2003 with a grant from the National Human Genome Research Institute.

John Rinn GRD ’04, an assistant professor of stem cell and regenerative biology at Harvard University who was not part of Encode, said that the Human Genome Project left scientists with enormous quantities of unanalyzed information. The purpose of Encode, he said, was to decode those “uncharted territor[ies].”

“Like Magellan navigating the ocean, [Encode] set out to make maps of the genome,” Rinn said.

Every cell contains the entire genome, but only reads certain parts – for example, a liver cell reads only the section describing the liver, and disposes of the remainder of the genome, Rinn said.

Encode mapped the presence of certain regions containing “noncoding RNA,” which organizes and determines the activities of various cells by deciding which section of the genome is read for each cell. Scientists were surprised to discover that noncoding RNA exists in equal quantities as messenger RNA (mRNA) that plays a role in protein building.

Weissman said that the results will facilitate other genetic research.

“If you want to study an unknown gene, now you can look at [Encode] and see what kind of proteins bind to the DNA near it, or the control sites of nearby DNA,” Weissman said. “It saves individual laboratories from doing studies on single genes.”

The computing technologies developed for data storage and transfer on the Encode project have been applied to other projects: modEncode, which identified functional elements in C. elegans and Drosophila; and the 1000 Genome Project, which aims to sequence the genomes of a large number of people.

Weissman added that Encode is far from complete. The next step for scientists is to further investigate the role of noncoding RNA regions.

Joe Locker, a professor of pathology at the Albert Einstein College of Medicine, said the results have “barely scratched the surface.

“There’s a great deal of additional information that’s necessary to make it comprehensive,” he said.

According to Locker, Encode has become somewhat outdated, as technology has developed that allows much of the work in the field to be done more cheaply and sensitively.

Some interviewed noted that the results of Encode were not entirely new information. Rinn conducted similar research at Yale as a graduate student in 1999, where he mapped miniature noncoding regions. Encode, however, revealed conclusively that there was more activity than anticipated in those noncoding regions.

Weissman said he enjoyed the research, because “every time you come to a door, you open three more doors.”

The Encode project revealed that more than 80 percent of the “junk regions” in the human genome were actually functional regions.

Comments

  • yalengineer

    I’m impressed by the depth of research behind this article. Something I would have expected from the Yale OPA&C but not the YDN.

  • CharlieWalls

    I doubt that “…a liver cell reads only the section describing the liver, and disposes of the remainder of the genome, Rinn said” is a correct statement. The “remainder of the genome” remains but is not expressed. That is what epigenetics is all about! And noncoding RNA has indeed been investigated now for several years. The simultaneous publication of ~30 papers in several journals annotating the genome serves to emphasize the larger view and the enormity of the task ahead to comprehend fully function of DNA in the cell. ‘Genes expressing proteins’ will become the quaint idea of the 20th C.

    • yalengineer

      Considering that John Rinn essentially discovered lincRNAs, yes, he does know quite a bit abut epigenetics.