$10.5 million awarded to researchers to work on DNA encyclopedia

Stanford’s William Greenleaf, Michael Bassik, Michael Snyder, Jonathan Pritchard and Michael Cherry have won grants to work on the federally funded Encyclopedia of DNA Elements.

The National Human Genome Research Institute has awarded four grants, totaling $10.5 million, to five researchers at the School of Medicine to advance the work of the Encyclopedia of DNA Elements, or ENCODE.

The goal of ENCODE is to build a comprehensive parts list of the human genome, including both the parts that make up genes and the parts that influence gene activity. The grants are intended to fund four years of research in five labs and are part of a total of about $31.5 million that NHGRI plans to commit to ENCODE, pending the availability of funds.

The Stanford recipients and their grant amounts are:

  • Will Greenleaf, PhD, assistant professor of genetics; Michael Bassik, PhD, assistant professor of genetics; and Anshul Kundaje, PhD, assistant professor genetics and of computer science: $1.18 million
  • Mike Cherry, PhD, professor of genetics: $4.95 million
  • Michael Snyder, PhD, professor of genetics; Howard Chang, MD, PhD, professor of dermatology; Greenleaf; Yiing Lin, MD, PhD, assistant professor of surgery at Washington University; and Kevin White, PhD, professor of human genetics and of ecology and evolution at the University of Chicago: $3.81 million
  • Jonathan Pritchard, PhD, professor of genetics and of biology; Bassik; Kundaje; and Stephen Montgomery, PhD, assistant professor of genetics and of pathology: $558,000 

Although scientists now know in detail the sequences of the genes that make up the genome, comparatively little is known about what the different genes do and how they work together. In particular, DNA sequences that code for polypeptides, which make up proteins, differ dramatically in function from so-called regulatory DNA sequences, which alter the activity of the coding genes.

The Pritchard lab will work on closing the gap between our understanding of coding DNA and the regulatory DNA. The team will, for example, develop a suite of tools, such as new machine-learning methods to identify genetic variants in the regulatory genes.

Greenleaf and Bassik will lead a “characterization center,” one of five nationwide, to study how the regulatory DNA functions and how cells with altered gene activity grow under a variety of conditions. The goal is to better understand how regulatory genes influence the activity of coding genes.

Cherry’s lab will continue to manage the ENCODE Data Coordinating Center at Stanford, which supports the ENCODE Consortium. The lab’s work provides the greater biological research community with different ways of cooperatively accessing all the data. In addition, the center will provide multiple services, including written documentation, video tutorials, webinars and meeting presentations.

Snyder’s grant will fund the Stanford ENCODE Production Center for Mapping of Regulatory Regions, where researchers will, among other things, map the binding sites for most of the gene activity that regulates molecules called transcription factors in five cell lines. The work will expand the catalog of known regulatory molecules in the human genome.



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