With sequencing of the human genome completed, attention is focusing on understanding gene function, which for approximately half of all genes remains unknown. A crucial first step is to determine spatial and temporal patterns of gene expression. This is especially important for early stages of embryogenesis, when many important developmental processes occur and when genes critical for normal development are expressed. Since gene expression analysis in human embryos is ethically untenable, mapping of expression patterns must be accomplished in model organisms. Chicken is the premiere non-mammalian model organism, and is used in research across a broad spectrum of research disciplines. The chicken embryo provides many advantages for large-scale expression screening, including striking similarities to human, low expense and ready availability. The goal of this proposal is to create an in situ hybridization expression resource for chicken embryos. The objectives are as follows: 1) to expand an existing gene expression screening effort, called GEISHA (gallus est in situ hybridization analysis), using automated high throughput whole mount in situ hybridization analysis to map the location of expressed sequences in chick embryos through four days of development; 2) to acquire additional expression data through parallel coordinated screening efforts, from individual researchers, and from published results; 3) to house expression information in a relational database and present expression data to the research community using a freely accessible web interface. A chicken anatomical ontology will be created to describe expression patterns and to enable spatio-temporal querying, and data will be used to annotate the chicken genome. This centralized repository for in situ hybridization gene expression information will provide a valuable and comprehensive resource for the biomedical research community.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Project (R01)
Project #
5R01HD044767-04
Application #
7556300
Study Section
Genome Study Section (GNM)
Program Officer
Coulombe, James N
Project Start
2005-01-01
Project End
2009-12-31
Budget Start
2008-01-01
Budget End
2008-12-31
Support Year
4
Fiscal Year
2008
Total Cost
$743,054
Indirect Cost
Name
University of Arizona
Department
Anatomy/Cell Biology
Type
Schools of Medicine
DUNS #
806345617
City
Tucson
State
AZ
Country
United States
Zip Code
85721
Darnell, Diana K; Stanislaw, Stacey; Kaur, Simran et al. (2010) Whole mount in situ hybridization detection of mRNAs using short LNA containing DNA oligonucleotide probes. RNA 16:632-7
Tsukada, Takehiro; Pappas, Christopher T; Moroz, Natalia et al. (2010) Leiomodin-2 is an antagonist of tropomodulin-1 at the pointed end of the thin filaments in cardiac muscle. J Cell Sci 123:3136-45
Antin, Parker B; Pier, Maricela; Sesepasara, Terry et al. (2010) Embryonic expression of the chicken Kruppel-like (KLF) transcription factor gene family. Dev Dyn 239:1879-87
Warkman, Andrew S; Yatskievych, Tatiana A; Hardy, Katharine M et al. (2008) Myocardin expression during avian embryonic heart development requires the endoderm but is independent of BMP signaling. Dev Dyn 237:216-21
Hardy, Katharine M; Garriock, Robert J; Yatskievych, Tatiana A et al. (2008) Non-canonical Wnt signaling through Wnt5a/b and a novel Wnt11 gene, Wnt11b, regulates cell migration during avian gastrulation. Dev Biol 320:391-401
Antin, P B; Kaur, S; Stanislaw, S et al. (2007) Gallus expression in situ hybridization analysis: a chicken embryo gene expression database. Poult Sci 86:1472-7
Darnell, D K; Kaur, S; Stanislaw, S et al. (2007) GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenet Genome Res 117:30-5
Darnell, Diana K; Kaur, Simran; Stanislaw, Stacey et al. (2006) MicroRNA expression during chick embryo development. Dev Dyn 235:3156-65
Ason, Brandon; Darnell, Diana K; Wittbrodt, Beate et al. (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci U S A 103:14385-9
Doyle, Sally E; Scholz, Matthew J; Greer, Kevin A et al. (2006) Latrophilin-2 is a novel component of the epithelial-mesenchymal transition within the atrioventricular canal of the embryonic chicken heart. Dev Dyn 235:3213-21