New Technology Helps Map Genome Expression

A strand of double-stranded DNA, in the shape of a double helix.
A strand of double-stranded DNA, in the shape of a double helix. (Image credit: James. J. Caras, National Science Foundation)

This Research in Action article was provided to LiveScience in partnership with the National Science Foundation.

Thanks to a substantial drop in the cost of DNA sequencing, a human genome, and the new supercomputers and next-generation gene sequencers, scientists are better understanding our DNA and how biological systems and disease relate.

Vishy Iyer of the University of Texas and his colleagues are beginning to investigate transcription factor proteins and their role in gene sequencing. The proteins bind to and regulate genes — turning a gene off or on and determining the activity level of the gene. Understanding how those proteins regulate genes will assist the study of diseases.

Using supercomputers and gene-sequencers, Iyer and colleagues at Duke, the University of North Carolina-Chapel Hill and Hinxton in the UK determined that transcription-factor binding is affected by differences in DNA and that those differences can be inherited.

The team concentrated only on the sections of DNA where the transcription factor proteins bind. ChIP-Seq, a sequencing technology, generated sequence reads containing the order of the nucleotides — molecules that link to form the building blocks of DNA or RNA — and the number of molecules bound. The Ranger Supercomputer, funded by the National Science Foundation, aligned the reads to the reference genome. Scientists could then study how genes and transcription proteins bind on a chromosome by looking at the known differences in DNA shown on the sequence reads.

This research has the potential to enable personalized medicine based on an individual's genome.

For the full story, see the Behind the Scenes article, "Placing Landmarks on the Genome Map."

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation. See the Research in Action archive.

National Science Foundation