The National Human Genome Research Institute (NHGRI) is a branch of the NIH, and they administer the ENCODE project, which stands for Encyclopedia of DNA Elements. Established in 2003, the goal of ENCODE is to create a comprehensive catalog of functional genomic elements. Towards that end, they have just awarded a further $10.5M in grants to 10 research institutions with investigators working in three main areas:
Discovery of Functional Elements
- University of Michigan, Ann Arbor; Mats Ljungman, Ph.D.; $1.2M to use bromouridine labeling of RNA towards development of new assays to identity promoters and enhancers and to measure mRNA degradation and splicing kinetics.
- University of Washington School of Medicine; Raymond David Hawkins, Ph.D.; $460K to improve the power of ChIP-seq assays to identify functional elements.
- MIT; Christopher Burge, Ph.D.; $800K to develop a new technology to catalog all of the RNA branch points that form in mRNA during splicing.
Validating the Biological Role of Functional Elements
- Washington University in St. Louis; Barak Cohen, Ph.D.; $1.1M to develop a method to test tens of thousands of promoters in primary cells.
- University of California Davis; Peggy Farnham, Ph.D.; $540K to test the function of genomic regions that bind large numbers of regulatory proteins.
- University of North Carolina at Chapel Hill; Jason Lieb, Ph.D.; $1.3M to develop a method to test tens of thousands of regions of open chromatin for enhancer, promoter, insulator and silencer activity.
- The Broad Institute of MIT and Harvard; Tarjei Sigurd Mikkelsen, Ph.D.; $1.1M to test tens of thousands of elements in integrated reporters, for enhancer activity, insulator function and RNA processing regulation.
- University of Washington, Seattle; Jay Shendure, M.D., Ph.D.; $1.9M to develop methods to capture or synthesize tens of thousands of regulatory elements, and test them in cell lines and mice.
Computational Analysis
- Memorial Sloan-Kettering Cancer Center, New York City; Christina Leslie, Ph.D.; $1.6M to develop new computational approaches to understand cell-specific gene expression programs, modeling cell-specific transcription as a function of chromatin state and transcription factor binding.
- Dana-Farber Cancer Institute, Boston; Guo-cheng Yuan, Ph.D.; $530K to develop novel computational methods to characterize chromatin states and predict chromatin interactions from these states.
According to NHGRI director Eric D. Green, M.D., Ph.D:
"The ENCODE project is providing a Rosetta Stone to understand how the sequence of the human genome forms the words that tell our bodies how to work at the molecular level. By developing more revolutionary technologies for probing genome function, we expect to accelerate these efforts."
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