The Developmental Genomics Section has been using a combination of zebrafish genetics and molecular embryology to study ear and hearing development. We have focused our attention on the study of several lines isolated in a screen for embryonically lethal mutations in zebrafish. Two of these mutations are being actively studied. The first is a mutation is in the zebrafish ortholog of the mouse gene Oct4. This gene is essential for maintaining stem cell pluripotency. We have performed transcriptional profiling in mouse ES cells and zebrafish embryos after modulating Oct4 levels. We are now in the process of perfoming ChIP-chip studies to establish the direct targets of Oct4 and their relationship to cell differentiation. The second mutation affects the regenerative ability in several tissues of the zebrafish embryo including the hair cells of the inner ear. We are cloning the transcript and establishing the subcellular localization of the protein and determining the function for the protein. Another focus of the lab is to develop tools for studying gene expression on a genome wide scale. We have developed a technique for rapidly mapping the integration sites for retroviruses and transposable elements and used that technique to define the global genomic profiles for MLV, HIV-1, and Sleeping Beauty based vectors. We are now in the second phase of a process to map thousands of proviral integrations in the zebrafish germline to create an archived zebrafish mutant resource. This phase will establish the framework for generating the resource and determine the number of total fish necessary to map 100,000 retroviral integrations.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Intramural Research (Z01)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Human Genome Research
United States
Zip Code
Liang, Jin; Burgess, Shawn M (2009) Gross and fine dissection of inner ear sensory epithelia in adult zebrafish (Danio rerio). J Vis Exp :
Gomez, Gustavo A; Veldman, Matthew B; Zhao, Yan et al. (2009) Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish. PLoS One 4:e4994
Jao, Li-En; Burgess, Shawn M (2009) Production of pseudotyped retrovirus and the generation of proviral transgenic zebrafish. Methods Mol Biol 546:13-30
Wang, Ting; Zeng, Jue; Lowe, Craig B et al. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A 104:18613-8
Wang, Dongmei; Jao, Li-En; Zheng, Naizhong et al. (2007) Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proc Natl Acad Sci U S A 104:12428-33
Wu, Xiaolin; Luke, Brian T; Burgess, Shawn M (2006) Redefining the common insertion site. Virology 344:292-5
Antonellis, Anthony; Lee-Lin, Shih-Queen; Wasterlain, Amy et al. (2006) Functional analyses of glycyl-tRNA synthetase mutations suggest a key role for tRNA-charging enzymes in peripheral axons. J Neurosci 26:10397-406
Ahmed, Zubair M; Goodyear, Richard; Riazuddin, Saima et al. (2006) The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15. J Neurosci 26:7022-34
Yan, Jizhou; Xu, Lisha; Crawford, Gregory et al. (2006) The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure. Mol Cell Biol 26:155-68
Nakai, Hiroyuki; Wu, Xiaolin; Fuess, Sally et al. (2005) Large-scale molecular characterization of adeno-associated virus vector integration in mouse liver. J Virol 79:3606-14

Showing the most recent 10 out of 21 publications