This Center of Excellence in Genomic Science (CEGS) assembles a multidisciplinary group of investigators to develop innovative technologies with the goal of imaging and mutating every developmentally important vertebrate gene. Novel """"""""in toto imaging"""""""" tools make it possible to use a systems-based approach for analysis of gene function in developing vertebrate embryos in real time and space. These tools can digitize in vivo data in a systematic, high-throughput, and quantitative fashion. Combining in toto imaging with novel gene traps permits a means to rapidly screen for developmentally relevant expression patterns, followed by the ability to immediately mutagenize genes of interest. Initially, key technologies will be developed and tested in the zebrafish embryo due to its transparency and the ability to obtain rapid feedback. Once validated, these techniques will be applied to an amniote, the avian embryo, due to several advantages including accessibility and similarity to human embryogenesis. Finally, to monitor alterations in gene expression in normal and mutant embryos, we will develop new techniques for in situ hybridization that permit simultaneous analysis of multiple marker genes in a sensitive and potentially quantitative manner. Our goal is to combine real time analysis of gene expression on a genome-wide scale coupled with the ability to mutate genes of interest and examine global alterations in gene expression as a result of gene loss. Much of the value will come from the development of new and broadly applicable technologies. In contrast to a typical technology development grant, however, there will be experimental fruit emerging from at least two vertebrate systems (zebrafish and avian). The following aims will be pursued:
Specific Aim 1 : Real-time """"""""in toto"""""""" image analysis of reporter gene expression.
Specific Aim 2 : Comprehensive spatiotemporal analysis of gene function of the developing vertebrate embryo using the FlipTrap approach for gene trapping.
Specific Aim 3 : Design of quantitative, multiplexed 'hybridization chain reaction'(HCR) amplifiers for in vivo imaging with active background suppression.
Specific Aim 4 : Data analysis and integration of data sets to produce a """"""""digital"""""""" fish and a """"""""digital"""""""" bird. The technologies and the resulting atlases will be made broadly available via electronic publication.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Specialized Center (P50)
Project #
Application #
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Felsenfeld, Adam
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
California Institute of Technology
Schools of Arts and Sciences
United States
Zip Code
Hochgreb-Hägele, Tatiana; Koo, Daniel E S; Bronner, Marianne E (2015) Znf385C mediates a novel p53-dependent transcriptional switch to control timing of facial bone formation. Dev Biol 400:23-32
Ruf-Zamojski, Frederique; Trivedi, Vikas; Fraser, Scott E et al. (2015) Spatio-Temporal Differences in Dystrophin Dynamics at mRNA and Protein Levels Revealed by a Novel FlipTrap Line. PLoS One 10:e0128944
Huss, David; Benazeraf, Bertrand; Wallingford, Allison et al. (2015) A transgenic quail model that enables dynamic imaging of amniote embryogenesis. Development 142:2850-9
Hochgreb-Hägele, Tatiana; Koo, Daniel E S; Das, Neha M et al. (2014) Zebrafish stem/progenitor factor msi2b exhibits two phases of activity mediated by different splice variants. Stem Cells 32:558-71
Sadowski, John P; Calvert, Colby R; Zhang, David Yu et al. (2014) Developmental self-assembly of a DNA tetrahedron. ACS Nano 8:3251-9
Saxena, Ankur; Bronner, Marianne E (2014) A novel HoxB cluster protein expressed in the hindbrain and pharyngeal arches. Genesis 52:858-63
Xiong, Fengzhu; Ma, Wenzhe; Hiscock, Tom W et al. (2014) Interplay of cell shape and division orientation promotes robust morphogenesis of developing epithelia. Cell 159:415-27
Hochgreb-Hagele, Tatiana; Bronner, Marianne E (2013) A novel FoxD3 gene trap line reveals neural crest precursor movement and a role for FoxD3 in their specification. Dev Biol 374:1-11
Saxena, Ankur; Peng, Brian N; Bronner, Marianne E (2013) Sox10-dependent neural crest origin of olfactory microvillous neurons in zebrafish. Elife 2:e00336
Hochgreb-Hagele, Tatiana; Yin, Chunyue; Koo, Daniel E S et al. (2013) Laminin *1a controls distinct steps during the establishment of digestive organ laterality. Development 140:2734-45

Showing the most recent 10 out of 50 publications