IBM Discovery Could Shed New Light on Workings of the Human Genome

As reported today in the Proceedings of the National Academy ofSciences (PNAS), regions of the human genome that were assumed tolargely contain evolutionary leftovers (called "junk DNA") mayactually hold significant clues that can add to scientists'understanding of cellular processes. IBM researchers have discoveredthat these regions contain numerous, short DNA "motifs," or repeatingsequence fragments, which also are present in the parts of the genomethat give rise to proteins.

If verified experimentally, the discovery suggests a potentialconnection between these coding and non-coding parts of the humangenome that could have a profound impact on genomic research andprovide important insights on the workings of cells.

"Our goal is to apply advanced computational techniques to analyzethe workings of processes and systems, in this case the function ofthe human genome," said Ajay Royyuru, head of the ComputationalBiology Center at IBM Research. "Using these tools, we've been able toshed new light on parts of the DNA that were traditionally thought ofas not having a specific purpose. We believe the innovativeapplication of technology can provide further understanding in thelife sciences at large."

The IBM team used a mathematical tool called pattern-discovery,often applied to mine useful information from very large repositoriesof data in both business and scientific applications, to sift throughthe approximately six billion letters in the non-coding regions of thehuman genome and look for repeating sequence fragments, or motifs.

Among the millions of discovered motifs, the team identifiedapproximately 128,000 that also occur in the coding region of thegenome and are significantly over-represented in genes involved inspecific biological processes such as cell communication, regulationof transcription, transport and others. In fact, copies of one or moreof these motifs can be found in over 90 percent of all known humangene sequences, as well as some genes of other animals where theyassociate with similar biological processes.

The report on this work, "Short blocks from the non-coding partsof the human genome have instances within nearly all known genes andrelate to biological processes," by Isidore Rigoutsos, Tien Huynh,Kevin Miranda, Aristotelis Tsirigos, Alice McHardy and Daniel Platt ofIBM's T. J. Watson Research Center, Yorktown Heights, NY appeared onApril 24th in the early edition of the journal PNAS.

About the IBM Research Division

IBM Research is the world's largest information technologyresearch organization, with about 3,000 scientists and engineers ineight labs in six countries. IBM has produced more researchbreakthroughs than any other company in the IT industry. For moreinformation on IBM Research, visit http://www.research.ibm.com.

Additional information is available athttp://www.research.ibm.com/bioinformatics/