NIH ENCODE grants advance effort to survey entire human instruction book

Grants totaling $30.3 million in fiscal year 2012 will expand the ENCyclopedia Of DNA Elements (ENCODE), a comprehensive catalog of functional elements that control the expression of genetic information in a cell, the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, announced today. The ENCODE project's goal is to provide the scientific community with information they need to better understand the role that the genome plays in health and disease.
“These grants build on the momentum of recently released ENCODE findings in which researchers provided a highly detailed and global view of the human genome,” said Elise A. Feingold, Ph.D., program director for ENCODE in NHGRI's Division of Extramural Research. “We have already made tremendous progress, but much work remains to complete the catalog of functional elements. These grants, awarded over a four-year period, will allow us to build on those results and take the next significant steps in deepening our understanding of the entire human genome.”
The new grants will advance ENCODE by expanding its investigation of functional elements to a considerably larger number of human cells and tissues, and a deeper set of data types. Analysis of the mouse genome, which had been a relatively small component of ENCODE, will also be expanded. The goal is to enhance use of this model organism in studying a wide range of tissues not readily accessible in the human, and to tap into the power of comparative genomic analysis to increase understanding of function of the human genome.
NHGRI will also establish a data coordinating center and a data analysis center, which together will make the ENCODE data more useful to the scientific community. New efforts will be supported to develop novel computational methods to improve analysis of ENCODE data and to make the data more useful for the study of human biology and disease.
All of the data generated by the ENCODE project will be deposited into public databases as soon as they are experimentally verified (http://encodeproject.org/ENCODE

). Free and rapid access to these data will enable researchers around the world to pose new questions and gain new insights into how the human genome functions. For more information about the ENCODE project, please visit http://www.genome.gov/ENCODE.
Recipients of awards are:
ENCODE Production Centers

Bradley Bernstein, M.D., Ph.D., Broad Institute, Cambridge, Mass. This group will catalog chromatin structure in human cells by mapping histone modifications as well as the proteins that direct these modifications. In living cells, DNA is packaged into chromatin by histone proteins; chromatin regulates access to information contained in DNA. Modifications to the histone proteins can affect cellular function. This award will continue work that Dr. Bernstein's group conducted in the previous phase of ENCODE.
Thomas Gingeras, Ph.D., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. This group will identify protein-coding and non-protein-coding ribonucleic acid (RNA) transcripts in human cells using high-throughput sequencing technology. The information in DNA is copied into RNA, an information molecule vital to a number of biological functions, especially protein production. This award will continue work that Dr. Gingeras' group conducted in the previous phase of ENCODE.
Brenton Graveley, Ph.D., University of Connecticut Health Center, Farmington. This group will analyze human RNA transcripts to identify protein binding sites, and to investigate their function. Proteins that bind to RNA can directly regulate protein production from RNA molecules, as well as affect protein production by regulating the degradation of RNA molecules. This work represents ENCODE's first production scale effort to map protein binding sites in RNA.
Richard Myers, Ph.D., HudsonAlpha Institute for Biotechnology, Huntsville, Ala. This group has three goals: to identify transcription factor binding sites in the human genome, to identify RNA transcripts in human and mouse cells and to identify the DNA methylation sites in the human genome. Transcription factors are proteins that regulate the process of copying information from DNA to RNA at individual genes. DNA methylation is a chemical modification of DNA that cells use to regulate gene expression. This award will continue work that Dr. Myers' group conducted in the previous phase of ENCODE.
Bing Ren, Ph.D., Ludwig Institute for Cancer Research, La Jolla, Calif. This group's project has two main goals: to map histone modifications and to identify DNA methylation sites, both in the mouse genome. These studies will build upon work that Dr. Ren's group has conducted under R01 research support.
Michael Snyder, Ph.D., Stanford University School of Medicine, Stanford, Calif. This group will identify transcription factor binding sites in the human genome. Dr. Snyder's and Dr. Myers' groups will coordinate efforts to map binding sites for the more than 1,500 transcription factors in the human genome. This award will continue work that Dr. Snyder's group conducted in the previous phase of ENCODE.
John Stamatoyannopoulos, M.D., University of Washington, Seattle. This group will map chromatin structure in the human and mouse genomes. This group will use DNase I, an enzyme that cleaves DNA where it is made accessible by transcription factor binding. These sites often mark the location of regulatory elements, or switches, in the genome. This award will continue work that Dr. Stamatoyannopoulos'group conducted in the previous phase of ENCODE.

ENCODE Data Coordination Center

J. Michael Cherry, Ph.D., Stanford University, Palo Alto, Calif. This group will work with the data production centers to collect, organize and store ENCODE data, and provide the research community access to data from the ENCODE Project.

ENCODE Data Analysis Center

Zhiping Weng, Ph.D., University of Massachusetts Medical School, Worcester. This group will work with the data production centers to perform integrated analyses of ENCODE data, and to make it easier for any researcher to use the data, including those studying human biology and specific diseases.

ENCODE Computational Analysis Awards

Peter Bickel, Ph.D., University of California, Berkeley. This group will develop new statistical and computational approaches to reduce the complexity of ENCODE data and to allow comparisons involving many ENCODE datasets at once.
David Gifford, Ph.D., Massachusetts Institute of Technology, Cambridge. This group will develop new computational approaches to identify regulatory elements in ENCODE data, and to learn how the components within each regulatory element work together.
Sunduz Keles, Ph.D., University of Wisconsin, Madison. This group will develop statistical methods and software to identify regulatory elements in the human genome, especially in sequences that are repeated at several locations.
Robert Klein, Ph.D., Sloan-Kettering Institute for Cancer Research, New York City. This group will develop new computational approaches to identify cell types and genetic changes responsible for human disease, using ENCODE data.
Jonathan Pritchard, Ph.D., University of Chicago. This group will develop new computational approaches to determine how changes in DNA sequence lead to changes in gene expression.
Xinshu Grace Xiao, Ph.D., University of California, Los Angeles. This group will identify genetic differences that alter RNA processing. When information is copied from DNA into RNA, one critical step is that the RNA is processed to remove information that is no longer required; without this processing, the RNA often cannot be used to make protein.

NHGRI is one of the 27 institutes and centers at NIH. The NHGRI Division of Extramural Research supports grants for research and training and career development at sites nationwide. Additional information about NHGRI can be found at http://www.genome.gov.
About the National Institutes of Health (NIH): NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

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