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NHGRI Awards $10.5M for New ENCODE Studies

NEW YORK (GenomeWeb News) – The National Human Genome Research Institute said today that it has awarded $10.5 million into studies aiming to develop new technologies for identifying functional genomic elements.

The new projects were funded under the Encyclopedia of DNA Elements, or ENCODE, project, a long-term effort launched in 2003 to create a catalog of functional elements in the human genome, and which last year received $123 million to continue to expand.

The 10 projects receiving funding will seek to develop new technologies for advancing ENCODE's mission, such as studies to develop new assays and improve others for identifying functional elements, validate biological elements by improving throughput and accuracy, and create new computational analysis tools predict protein and chromosomal interactions and behaviors.

"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," NHGRI Director Eric Green said in a statement. "By developing more revolutionary technologies for probing genome function, we expect to accelerate these efforts."

"The current ENCODE efforts owe a good part of their success to technology development that has occurred over the last decade," added Elise Feingold, a program director for ENCODE in NHGRI's Division for Extramural Research. "In addition to the technologies developed through this program, ENCODE has benefitted enormously from advances fostered by NHGRI's DNA sequencing technology initiative, the $1000 Genome Program."

Three of the new grants will fund tools for discovering functional genomic elements, including $800,000 to Christopher Burge of the Massachusetts Institute of Technology to develop a tool for cataloging all of the RNA branch points that form in mRNA during splicing; $1.2 million to the University of Michigan's Mats Ljungman to develop new assays to identify promoters and enhancers and to measure mRNA degradation and splicing kinetics; and $460,000 to Raymond Hawkins of the University of Washington School of Medicine to improve the power of ChIP-seq assays, among the most fundamental assays used in ENCODE studies, to identify functional elements in the genome that are attached to a particular protein.

Five of the new grants will fund studies to validate the biological role of functional elements, including $1.1 million to Washington University in St. Louis scientist Barak Cohen to develop a method to test tens of thousands of promoters in primary cells; $540,000 to Peggy Farnham of the University of Southern California to test the function of genomic regions that bind large numbers of regulatory proteins; $1.3 million to University of North Carolina at Chapel Hill researcher Jason Lieb to develop a method to test tens of thousands of regions of open chromatin for enhancer, promoter, insulator, and silencer activity; $1.1 million to Tarjei Mikkelsen at the Broad Institute of MIT and Harvard to test tens of thousands of elements for enhancer activity, insulator function, and RNA processing regulation; and $1.9 million to Jay Shendure of the University of Washington and Nadav Ahituv of UC San Francisco to capture or synthesize tens of thousands of regulatory elements and test them in cell lines and mice.

Two other research projects will fund computational analysis studies, including $1.6 million to researcher Christina Leslie at Memorial Sloan-Kettering Cancer Center to develop new computational approaches to understand cell-specific gene expression programs and modeling cell-specific transcription as a function of chromatin state and transcription factor binding; and $530,000 to Guo-cheng Yuan of Dana-Farber Cancer Institute to develop computational methods to characterize chromatin states and predict chromatin interactions from these states.

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