Our long term goal is to understand early vertebrate development at the molecular level. We study the problem in the frog Xenopus, whose abundant eggs are large and readily manipulated by microinjection and microsurgery. The eggs are large enough to produce material for biochemical analysis, and importantly for this project, ample RNA from manipulated embryos for deep sequencing. A combination of experimental embryology and molecular manipulation provides approaches to the roles of specific signaling pathways, transcriptional and post- transcriptional regulation in elaborating the structure of the embryo. Most of the paradigms for development of vertebrate embryos have come first from work with amphibians, and many of the signaling pathways were first analyzed using amphibian embryos. Gain of function experiments using mRNA injection, and loss of function using morpholino oligonucleotides have provided insights into the mechanisms that underlie tissue differentiation and morphogenesis. During previous grant periods, we have used expression cloning to identify potent signaling and signal transduction activities that contribute to embryoni development. In screens for embryonic activities that alter neural patterning we identified several RNA regulators that show specific effects in both gain of function and loss of function experiments. We have established methods to study both splicing regulation and changes in gene expression using deep sequencing.
In aim 1 of the next grant period, we will continue analysis of selected RNA binding and pre-mRNA splice regulators that are deployed during the induction and patterning of the neural plate, and will continue to gain new insight into the selective effect of these proteins on specific splicing choices. In addition to splicing regulation we will also study transcription factors, and chromatin regulators whose expression are altered during neural patterning, and will particularly investigate factors that are turned on by the Wnt pathway during posterior patterning of the neural plate.

Public Health Relevance

Human diseases are frequently associated with aberrant function of genes normally used in early development. Here we will understand the function of gene products that act in patterning of the nervous system, including transcriptional regulators, and proteins that process pre- mRNAs.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01GM042341-28
Application #
8706885
Study Section
Development - 1 Study Section (DEV1)
Program Officer
Hoodbhoy, Tanya
Project Start
Project End
Budget Start
Budget End
Support Year
28
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Young, John J; Kjolby, Rachel A S; Wu, Gloria et al. (2016) Noggin is required for first pharyngeal arch differentiation in the frog Xenopus tropicalis. Dev Biol :
Walentek, Peter; Quigley, Ian K; Sun, Dingyuan I et al. (2016) Ciliary transcription factors and miRNAs precisely regulate Cp110 levels required for ciliary adhesions and ciliogenesis. Elife 5:
Rochard, Lucie; Monica, Stefanie D; Ling, Irving T C et al. (2016) Roles of Wnt pathway genes wls, wnt9a, wnt5b, frzb and gpc4 in regulating convergent-extension during zebrafish palate morphogenesis. Development 143:2541-7
Kjolby, Rachel A S; Harland, Richard M (2016) Genome-wide identification of Wnt/β-catenin transcriptional targets during Xenopus gastrulation. Dev Biol :
Dichmann, Darwin S; Walentek, Peter; Harland, Richard M (2015) The alternative splicing regulator Tra2b is required for somitogenesis and regulates splicing of an inhibitory Wnt11b isoform. Cell Rep 10:527-36
Walentek, Peter; Beyer, Tina; Hagenlocher, Cathrin et al. (2015) ATP4a is required for development and function of the Xenopus mucociliary epidermis - a potential model to study proton pump inhibitor-associated pneumonia. Dev Biol 408:292-304
Werner, Achim; Iwasaki, Shintaro; McGourty, Colleen A et al. (2015) Cell-fate determination by ubiquitin-dependent regulation of translation. Nature 525:523-7
Jang, Dong Gil; Sim, Hyo Jung; Song, Eun Kyung et al. (2015) A thioredoxin fold protein Sh3bgr regulates Enah and is necessary for proper sarcomere formation. Dev Biol 405:1-9
Plouhinec, Jean-Louis; Roche, Daniel D; Pegoraro, Caterina et al. (2014) Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers. Dev Biol 386:461-72
Chung, Hyeyoung A; Medina-Ruiz, Sofia; Harland, Richard M (2014) Sp8 regulates inner ear development. Proc Natl Acad Sci U S A 111:6329-34

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