Human disease often involves changes in the timing and level of gene expression, processes investigated by transcriptomics, the identification of each expressed gene and its transcriptional levels. Studies of the association of human variation with altered gene expression can lead to a deeper, mechanistic understanding of disease states and can suggest therapies. A promising route to discovery is the transcriptomic analysis of novel models of common human diseases in aquatic species for which few genomic resources presently exist. Breakthroughs in sequencing technologies have opened the door for transcriptomics in non-model organisms. As detailed at the Sept. 2010 workshop 'Realizing the Scientific Potential of Transcriptomics in Aquatic Models', several impediments currently hinder the successful use of these tools in aquatic model systems. The goal of this project is to overcome these barriers by developing the protocols and tools necessary for researchers to capitalize on recent advances in DNA sequencing technology to better perform transcriptome analyses on aquatic medical models. This project will develop optimal laboratory protocols, analytical theory and computational software for transcriptome analyses of aquatic models of human disease and will help researchers plan and analyze experimental results. Protocols and tools will be made available via the Galaxy web platform as easy-to-use interfaces for computational software and web-based tutorials. Because many researchers working with aquatic non-model organisms lack access to the latest sequencing facilities and computational expertise for the analysis of high throughput transcriptomics, mechanisms will be developed for aquatic model organism researchers to use the Univ. of Oregon High Throughput Sequencing Facility. Similarly, many researchers lack access to computer clusters sufficiently powerful to execute the computational demands of modern transcriptomics, so this project will increase the availability of computational pipelines running at the Univ. of Oregon. This project will therefore provide widely needed tools, raise barriers to progress, and improve methods and technologies for transcriptome analysis in aquatic medical models, thus advancing our understanding of the role of gene regulation in health and disease.

Public Health Relevance

Studies of gene expression in aquatic model organisms promise significant breakthroughs in our understanding of the genetic causes of human diseases that can significantly increase human health. This project will accelerate research on non-model aquatic organisms by developing best practices and tools, making resources and training available, providing resources for laboratories to generate and analyze new types of genetic data and by contributing to the training of computer scientists in bioinformatics.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
Resource-Related Research Projects (R24)
Project #
5R24OD011199-04
Application #
8711585
Study Section
Comparative Medicine Review Committee (RIRG)
Program Officer
Contreras, Miguel A
Project Start
2011-09-15
Project End
2015-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
4
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Oregon
Department
Biology
Type
Graduate Schools
DUNS #
City
Eugene
State
OR
Country
United States
Zip Code
97403
Boswell, Mikki; Boswell, William; Lu, Yuan et al. (2018) The transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes. Comp Biochem Physiol C Toxicol Pharmacol 208:77-86
Klotz, Barbara; Kneitz, Susanne; Regensburger, Martina et al. (2018) Expression signatures of early-stage and advanced medaka melanomas. Comp Biochem Physiol C Toxicol Pharmacol 208:20-28
Lu, Yuan; Boswell, Mikki; Boswell, William et al. (2018) Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions. Pigment Cell Melanoma Res 31:496-508
Boswell, William T; Boswell, Mikki; Walter, Dylan J et al. (2018) Exposure to 4100K fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol 208:96-104
Walter, Ronald B; Boswell, Mikki; Chang, Jordan et al. (2018) Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus). BMC Genomics 19:355
Pasquier, Jeremy; Braasch, Ingo; Batzel, Peter et al. (2017) Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome. J Exp Zool B Mol Dev Evol 328:709-721
Cal, Laura; MegÍas, Manuel; Cerdá-Reverter, José Miguel et al. (2017) BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish. J Exp Zool B Mol Dev Evol 328:697-708
Lu, Yuan; Boswell, Mikki; Boswell, William et al. (2017) Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog 56:1935-1944
Small, C M; Bassham, S; Catchen, J et al. (2016) The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 17:258
Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J et al. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 48:427-37

Showing the most recent 10 out of 46 publications