Professor Thomas Tullius, chairman of the Chemistry Department, has received a three-year, $870,000 grant from the National Human Genome Research Initiative to try to map the surface of naked DNA, or DNA without protein molecules bound to its surface.
Tullius' research is part of an international research effort called ENCODE, short for Encyclopedia of DNA Elements. ENCODE chose Tullius for his expertise in chemical probing - a method he has been perfecting in his lab over the past few years.
"What we do is treat a molecule with a hydroxyl radical, which chops up the DNA," Tullius said. "The variation in how it gets cut tells us about its shape."
Tullius is one of five principle investigators to receive technology development grants from the National Human Genome Research Institute, which is a part of the National Institutes of Health.
ENCODE Program Director Peter Good said the NHGRI recently published a paper about the completed human genome sequence, but said more research is necessary to figure out what the sequences mean.
"The problem is that we have the sequence, but we don't know what it is," he said.
Tullius said the encyclopedia would help researchers to better understand the human genome and its functional elements.
"The whole idea behind the ENCODE project is knowing the sequences," Tullius said. "We have very little idea what is going on in 95 to 98 percent of the genome, and our project is trying to find signals in the rest of the genome so that other things in the genome become known."
Tullius' grant comes in the second round of funding for technology-based research in contribution to ENCODE, according a BU press release.
Zhiping Weng, an associate BU professor of biomedical engineering, received a grant in the first round of funding.
"Two years ago, we put out a request for application, and we gave out grants for the first cycle, including Zhiping Weng," Good said. "We then decided that there was more technology out there, and Tom [Tullius] applied last year and we ended up funding him on October 1st of this year."
Good said Tullius was chosen after his application was peer-reviewed because of his expertise and approach to the research effort.
"[The peer review board] thought that Tullius' chemical probing was very innovative, and they thought that it was a very good collaboration with Weng," Good said.
Tullius said he has been working on this procedure in his lab for years with help from graduate students, as well as the assistance of six undergraduates in past summers.
"Graduate student Jay Greenbalm has designed a database based on the research done in that lab, and analyzed it to look for interesting patterns in these DNA cleavage," Tullius said.
One of the goals of Tullius' ENCODE research is to build a database of patterns of DNA's sequence and structure, according to a BU press release. He then plans to develop computational methods that can predict patterns in any sequence of DNA, and to use the experimental and computational approaches to build structural maps of the genome.
"We've gotten a fair way along on this," Tullius said. "[Greenbalm] came up with a data-mining way of predicting cleavage patterns."
The grant money will be used to support graduate students and to buy more equipment, Tullius said.
Other funding went to researchers at the Genome Institute of Singapore; Intronn, Incorporated in Gaithersburg, Md., The Research Foundation of the State University of New York, in Albany, N.Y., The Salk Institute in La Jolla, Calif. and the University of Texas in Austin, Texas.
Tullius said he will be going to Cold Spring Harbor Labs in Long Island, N.Y.. next week, where he and the other researchers will share information with each other.
"What is unique about this research effort is that it's a very cooperative project where the investigators get together a few times a year," Tullius said. "It's a different mode of working, working directly with other people."
The data from the ENCODE project will be put on the University of California, Santa Cruz genome browser, which uses all different tracks of data for human genome research.
"The data that comes from ENCODE will be put on the browser where people will try to figure out using diff kinds of viewpoints," Tullius said.
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