From left are lab technician Becky Cai, Molecular Biology and Genetics Graduate Program Ph.D. candidate Emily Wood, WSU Assistant Professor and ENCODE project co-investigator Leonard Lipovich, Ph.D., and postdoctoral fellow Hui Jia, Ph.D.
Researchers at the Wayne State University School of Medicine, led by Assistant Professor of Molecular Medicine and Genetics Leonard Lipovich, Ph.D., will contribute to the next generation of the National Institutes of Health’s ENCODE Consortium, announced Monday as the second large-scale research follow-up to the 2001 mapping of the human genome.
Grants totaling $30.3 million will expand the Encyclopedia of DNA Elements project, a comprehensive catalog of functional elements that control the expression of genetic information in a cell. The project’s goal is to provide the scientific community with information needed to better understand the role that the genome plays in health and disease.
In a collection of academic papers released in three scientific journals earlier this month, more than 400 researchers in 32 labs, working collaboratively for ENCODE around the world, produced an expansive atlas of functional elements in the human genome. Dr. Lipovich and members of his lab at WSU were among them. Now, his team at WSU’s Center for Molecular Medicine and Genetics will spend the next three years working with University of California, Berkeley Professor Peter Bickel, Ph.D., and his colleagues to develop and validate new statistical and computational approaches to reduce the complexity of ENCODE data, and to allow comparisons involving many ENCODE datasets at once.
Dr. Lipovich, a Detroit resident, is a co-investigator on the $1,341,270 project, “Removing Statistical Bottlenecks in Data Analysis for the ENCODE Consortium.” The total WSU portion of this grant comprises $390,683. The funds will help support the necessary lab consumables, along with salaries and required travel costs, for Dr. Lipovich, his lab technician Becky Cai, who will conduct the experimental portion of the project, and Emily Wood, a doctoral candidate in the School of Medicine’s Molecular Biology and Genetics Graduate Program. Wood’s new computational method to analyze the experimental data will be used in the first year of the project.
Hui Jia, Ph.D., a postdoctoral fellow in the Lipovich lab, contributed one of the initial computational investigations needed for Dr. Lipovich and team to analyze data in phase one of ENCODE. As a result, Dr. Jia was a joint-first author of “Long noncoding RNAs are rarely translated in two human cell lines,” a paper published in the September issue of Genome Research as a part of the recently released collection of ENCODE academic papers.
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.
The UC-Berkeley/WSU team will use one of six ENCODE computational analysis grants recently awarded. The ENCODE Data Coordination and Analysis Center will be responsible for applying techniques to examine all consortium data, per the direction of ENCODE’s Analysis Working Group. The ENCODE AWG – in which Dr. Lipovich’s lab participated and provided computational analysis for the previous phase of ENCODE – was open to all academic, government and private sector scientists interested in participating in an open process to facilitate the comprehensive identification of the functional elements in the human genome sequence, and who agreed to a variety of criteria. Now, Dr. Lipovich joins a smaller group of ENCODE Consortium grant recipients and co-investigators who will implement the effort’s next phase.
Dr. Lipovich also is a member of the Japan-based international research consortium Functional Annotation of the Mammalian Genome, the other leading post-genome effort. FANTOM, headquartered at the RIKEN (Japan Institute of Physical and Chemical Research) Omics Science Center in Yokohama, analyzes the mammalian transcriptome – the complete set of all RNA molecules produced in one or a population of cells – using next-generation sequencing. The FANTOM participation exposed Dr. Lipovich to other valuable collaborations – such as ENCODE.
The Lipovich lab is the only laboratory in Michigan to participate in both FANTOM and ENCODE.
“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 humans, and to tap into the power of comparative genomic analysis to increase the understanding of function of the human genome.
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 the 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, visit http://www.genome.gov/ENCODE.This ENCODE grant – WSU’s first – places the university into a group that includes researchers from UC-Berkeley, Stanford University, the Massachusetts Institute of Technology, University of Chicago, The Broad Institute of MIT and Harvard University, and the Sloan-Kettering Institute for Cancer Research in New York City.