Rewriting the book on the human genome

After four years of research, an international effort finds that junk DNA may not be junk after all.

A study published in Nature last summer has revealed a much more complex view of the vast, uncharted regions of the human genome than previously supposed. “Junk DNA,” noncoding sequences that make up the bulk of the genome’s 3 billion letters, may indeed have a purpose. Now the challenge is to figure out what all that DNA is for. Doing so may prove crucial for understanding complex human diseases.

“We’re trying to map out what’s there,” said Michael Snyder, Ph.D., professor of molecular, cellular and developmental biology.

Snyder’s lab is part of the Encyclopedia of DNA Elements (ENCODE) project, a mammoth undertaking of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) involving 35 groups of researchers at 80 institutions in 11 nations. Researchers have spent the last four years sifting through more than 400 million data points to make sense of just 1 percent of the human genome. Their analysis has turned up some surprises.

For one thing, the genome hosts a lot more activity than expected. The conventional wisdom has long held that the important pieces of DNA—the readily decipherable genes making up 1.5 percent of the genome—are converted into RNA via a process called transcription. RNA in turn instructs the cell to make proteins. Scientists have long assumed that in general each gene is transcribed into one RNA fragment and that the remaining gene-free portions of our DNA aren’t transcribed at all.

Not so, according to the ENCODE project. Most letters in the genomic instruction manual wind up being transcribed. Each gene is often transcribed along with a surprisingly large number of nonprotein-coding (NPC) sequences to produce some extraordinarily long RNA fragments. A single gene can be transcribed into many different RNA fragments of varying lengths. The purpose of all these extra transcripts remains unclear.

Even more perplexing is the prevalence of RNA molecules transcribed entirely from gene-free portions of the genome. NPC RNA transcripts were previously known to exist, but the ENCODE project identified many new ones. Again, their purpose is unknown.

Snyder is even more excited that the project has identified new regulatory regions that do not encode proteins but instead control when, where and to what extent genes are expressed. Recent studies have linked complex diseases with variations in NPC regions of the human genome that could have regulatory functions. Might variations in NPC DNA promote disease by interfering with the expression of genes at distal sites?

Snyder and his collaborators hope that the project will answer such questions. “This is really what the ENCODE project is all about,” he said.

—Robin Orwant

A podcast of Michael Snyder speaking on this subject can be found on the Yale page on iTunes U. Visit itunes.yale.edu or launch iTunes, then select Yale from the offerings under iTunes U. The podcast is included under “Yale Science.”

An atomic view of a protein offers insights into a new target for cancer drugs

A research team led by Joseph Schlessinger, Ph.D., the William H. Prusoff Professor and chair of pharmacology, has solved the atomic-level structures for active and inactive forms of a protein segment implicated in several types of cancer, opening up a new set of molecular targets for cancer therapies.

The results, reported in the July 27 issue of Cell, highlighted previously unidentified changes in the protein’s structure that seem to be crucial for its activation. “It gives us totally new avenues for developing drugs for a large group of target proteins that are responsible for several cancers,” Schlessinger said.

The study focused on one of 59 receptor tyrosine kinases (RTKs), a set of related proteins whose activities have long been linked with cancer. Normally, RTKs become active only under particular circumstances in order to help cells proliferate, differentiate and survive. But certain mutations in RTKs can turn on the proteins inappropriately, causing aberrant cell proliferation that may lead to cancer. Blocking the activities of RTKs has become a major strategy in anticancer drug design.

Two recently developed and highly successful cancer-fighting drugs, Gleevec and Sutent, work in this way. Gleevec is effective against some stomach cancers and leukemias; Sutent works against stomach and some kidney cancers. But Schlessinger, who helped discover Sutent, said many cancers don’t respond to Gleevec or Sutent and those that do develop resistance to the drugs.

Schlessinger’s laboratory has spent the last 10 years assembling an atomic-level view of the extracellular domain of an RTK called Kit. By comparing the structure of the protein segment (representing Kit in its inactive state) with that of the active form, his research group has identified changes in Kit that are important in understanding its activation.

The results suggest that in their active state Kit molecules change their shape such that certain portions of the extracellular domain in one Kit molecule move close enough to interact with their counterparts on the other Kit molecule. Schlessinger and colleagues have also provided evidence that these previously unidentified interactions are required for Kit activation, and mutations predicted to strengthen the interactions are known to contribute to various forms of cancer.

Since Kit is part of a family of RTKs with similar extracellular domains, the targets represented by this study probably exist in more than a half-dozen other RTKs that have been implicated in various cancers. “It’s a mechanism that is likely to be universal to quite a few of these RTKs,” Schlessinger said.

Drugs aimed at these new targets might be effective against Gleevec- and Sutent-resistant cancers, offering hope to many cancer patients who are trying to stay one step ahead of the enemy.

—R.O.

et cetera

Nanotubes can kill bacteria

A study to measure the toxic effects of nanotubes on human cells has led to a possible new approach to treating antibiotic-resistant infections.

In a paper published in the August 28 issue of the American Chemical Society journal Langmuir, Yale researchers said that single-walled carbon nanotubes (SWCNTs) can kill such bacteria as E. coli.

“We began the study out of concern for the possible toxicity of nanotubes in aquatic environments and their presence in the food chain,” said Menachem Elimelech, Ph.D., the Roberto C. Goizueta Professor and chair of chemical engineering. “While nanotubes have great promise for medical and commercial applications, there is little understanding of how they interact with humans and the environment.”

Elimelech speculates that the long, thin nanotubes puncture the cells and cause cellular damage. “We are looking at the effects of SWCNTs on a wide range of bacterial strains to better understand the mechanism of cellular damage,” Elimelech said.

—John Curtis

To beat cancer, eat your veggies!

Kids aren’t the only people who should pile more vegetables on their dinner plate. A study published in the August 1 issue of JNCI: Journal of the National Cancer Institute shows that men who regularly eat broccoli, cauliflower, cabbage, Brussels sprouts and turnips are 40 percent less likely to develop advanced prostate cancer than those who consume few of these veggies.

“All these vegetables have compounds called glucosinolates that have been shown to protect cells from DNA damage in the lab, and thus may be anticarcinogenic,” said lead author Victoria Kirsh, Ph.D., a former doctoral student of Susan T. Mayne, Ph.D., professor of epidemiology. Kirsh is now at Cancer Care Ontario.

To make sure that men who consume more vegetables aren’t just more likely to get prostate screening tests than others, Kirsh used data that identified 1,338 men diagnosed with prostate cancer out of 29,361 who were screened.

—Sarah C.P. Williams


			Originally published in Yale Medicine, Winter 2008. Copyright © 2008 Yale University School of Medicine. All rights reserved.