Expression Profiling of Cellular Metabolism Using Massively Parallel Sequencing

Ut Southwestern Medical Center, Dallas TX

Investigators

Abstract

DESCRIPTION (provided by applicant): Next-generation sequencing (NGS) provides a powerful new technology to rapidly and effectively interrogate DNA sequence in a simple, comprehensive and cost-effective manner. Probing patterns of whole genome expression, defining the full panoply of genes targeted by transcription factors, and assessing genome-wide methylation status has become feasible and affordable using NGS. The goal of this grant is to establish a high through-put NGS Facility to support ongoing research projects by a thematically-linked cadre of scientists who have a history of implementing new technologies to make high- impact, fundamental discoveries with direct applications to human health. The research focuses on two major causes of death and disability: disorders of cholesterol metabolism and dysregulated fuel homeostasis. Funds are requested to purchase a Sequencing by Oligonucleotide Ligation and Detection (SOLiD) 3 System from Applied Biosystems. The instrument will be operated by the McDermott Center DNA Sequencing Core Laboratory. Initially, the NGS Facility will support investigators funded by two NIH- sponsored programmatic grants: a Program Project (The Molecular Basis of Cholesterol Metabolism) spearheaded by Drs. Michael Brown and Joseph Goldstein that is in its 32nd year of funding, and a new interdisciplinary Roadmap grant, the Taskforce for Obesity Research at UT Southwestern, which brings together 25 independent PI's from 16 different departments. This proposal is structured so that a group of 13 major users with strong scientific programs and a track record of making biologically significant observations will use the SOLiD 3 System to enhance experiments already funded by the NIH. Proposed studies include using gene expression profiling to interrogate the cellular responses to metabolic perturbations, CHiP-sequencing to identify target genes of key metabolic transcription factors discovered by PI's of this application, and DNA methylation profiling to assess the impact of diet on epigenetic programming. Given the scientific productivity of the PI's on this grant, we are optimistic that application of this technology will result in important new discoveries that will directly impact human health. Although the users of the NGS Facility will initially be limited to 13 investigators, the experience gleaned by these scientists will be rapidly disseminated to the entire UT Southwestern research community. We anticipate that both the scope of applications and the spectrum of users will expand in the near future and that the SOLiD System will become an integral part of the McDermott Center DNA Sequencing Core that has provided excellent university-wide service at UT Southwestern for over a decade.