$9 million NHGRI award to University of Chicago team will enable genome-wide discovery of the DNA sequences that regulate genes

The National Human Genome Research Institute, part of the National Institutes of Health, has awarded $9.1 million over four years to a research team led by the University of Chicago to identify all regulatory elements, the DNA sequences that control when and where specific genes get turned on or off, in the fruit fly genome.

The award is part of a $57-million scientific mission—the ENCyclopedia Of DNA Elements (ENCODE)—to understand every part of the genome needed for organisms to develop and survive. ENCODE was created to assemble a comprehensive catalog, or "parts list," of all functional elements in the human genome.

"Our project will serve as a pilot for the full-scale mapping of functional regulatory elements in the human genome," said program director Kevin White, PhD, the James and Karen Frank Family Professor in the departments of Human Genetics and Ecology & Evolution, and Director of the Institute for Genomics & Systems Biology at the University of Chicago and Argonne National Laboratory. [more info]

The goal of the Institute for Genomics & Systems Biology (IGSB) is to accelerate the transition of basic discoveries in genome science into practical benefits for society. The Institute bridges two extraordinary research communities: The University of Chicago and Argonne National Laboratories.

IGSB researchers are performing investigations of complex biological systems from a wide variety of perspectives — including experimental, computational and theoretical points of view.

IGSB research at the University of Chicago is focused on genomics and systems biology approaches to discover new diagnostic and therapeutic targets, strategies for complex human diseases and basic discoveries of genome function evolution. 

The IGSB is divided into ten different areas of investigation. IGSB resources are focused on the promotion of research in these ten areas, and investigators are invited to participate in one or more of these areas as they deem relevant to their own research programs.

Proteomics and Structural Genomics
Computational Biology and Informatics
Microbial Systems Biology
Evolutionary Genomics and Systems
Biological Engineering and Technology Development
Cellular and Genomic Networks
Chemical Genomics
Cancer
Population Genomics and Complex Diseases
Clinical Genomics

IGSB Initiatives 2008

Breast Cancer
Several screening projects are being performed in the Cellular Screening Center (CSC) as part of the Breast Cancer Initiative. Ruby Dhar, PhD (Human Genetics) and IGSB Director Kevin White, PhD (Human Genetics and Ecology & Evolution) initiated a study to understand the role of estrogen in breast cancer. They used RNA interference technology in the CSC to turn off the function of genes in breast cancer cell lines with the aim of assessing the role of specific genes and the rapid identification of novel drug targets. Several promising candidate genes have already been identified. Suzanne Conzen (Department of Medicine, Section of Hematology / Oncology) is also working with facility staff to screen a chemical library against breast cancer cell lines to develop improved, targeted therapies.

Metabolic Diseases and Diabetes
In partnership with the IGSB, Mark Ratain, MD (Department of Medicine, Section of Hematology / Oncology) and colleagues are analyzing genome wide variation in DNA sequence and gene expression in a large collection of human livers to discover patterns of genomic variation and expression. This comprehensive study, never before conducted, will provide the basis for evaluating potential outcomes of drug therapy in individual cancer patients. About 75% of the top 200 drugs prescribed are eliminated from the body through the metabolic enzymes in the liver. In addition to receiving seed funding as part of the IGSB Medtabolic Diseases and Diabetes Intiative, Ratain and colleagues are using the resources of the High Throughput Genome Analysis Core (HGAC) to perform their study. As part of the same Initiative, Chris Rhodes, PhD (Department of Medicine, Section of Endocrinology, Diabetes and Metabolism) is performing drug and genome screening of insulin-secreting cells in the CSC to identify therapies which promote insulin production in diabetes patients.

Inflammatory Bowel Disease
Eugene Chang, MD (Department of Medicine, Section of Gastroenterology) has partnered with IGSB Core Member Dion Antonopoulos, PhD (IGSB, Argonne) to sequence patient gut contents, containing thousands of different bacterial species, to determine the relationship between specific bacteria and inflammatory bowel disease. This metagenomics project has been supported by seed funding from the Institute’s Inflammatory Bowel Disease Initiative and takes advantage of the next generation sequencing technology within the HGAC, as well as the computational expertise at Argonne.