http://domino.research.ibm.com/comm/pr.nsf/pages/news.20060425_dna.html
IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.
As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNAâ€Â) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,†or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.
If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells.
“Our goal is to apply advanced computational techniques to analyze the workings of processes and systems, in this case the function of the human genome,†said Ajay Royyuru, head of the Computational Biology Center at IBM Research. “Using these tools, we’ve been able to shed new light on parts of the DNA that were traditionally thought of as not having a specific purpose. We believe the innovative application of technology can provide further understanding in the life sciences at large.â€Â
The IBM team used a mathematical tool called pattern-discovery, often applied to mine useful information from very large repositories of data in both business and scientific applications, to sift through the approximately six billion letters in the non-coding regions of the human genome and look for repeating sequence fragments, or motifs.
Among the millions of discovered motifs, the team identified approximately 128,000 that also occur in the coding region of the genome and are significantly over-represented in genes involved in specific biological processes such as cell communication, regulation of transcription, transport and others. In fact, copies of one or more of these motifs can be found in over 90 percent of all known human gene sequences, as well as some genes of other animals where they associate with similar biological processes.
The report on this work “Short blocks from the non-coding parts of the human genome have instances within nearly all known genes and relate to biological processes†by Isidore Rigoutsos, Tien Huynh, Kevin Miranda, Aristotelis Tsirigos, Alice McHardy and Daniel Platt of IBM’s T. J. Watson Research Center, Yorktown Heights, NY appeared on April 24th in the early edition of the journal PNAS.
http://www.pnas.org/cgi/content/abstract/0601688103v1
Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of {approx}22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For {approx}1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60-80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume {approx}40% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3′ UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.