Education & Training:
University of California, Berkeley (1988) BA in Physiology
University of Washington, Seattle (1993) PhD in Biochemistry
University of Oregon, Eugene (1999) Postdoctoral Fellow

Research Interests:
The goal of our research is to understand how genes control cell fate commitment and patterning, at the level of single cells, in the developing vertebrate embryo. We work at the intersection of genetics, cell biology, and developmental biology to study muscle development, from early specification during gastrulation, through segmental patterning, to muscle differentiation and disease, using the zebrafish as a model for human development and disease.

Mesodermal patterning. The embryonic mesoderm is specified during gastrulation, with dorsal mesoderm becoming notochord, lateral mesoderm forming muscle, and ventral mesoderm becoming blood. We are characterizing the molecular and cellular events involved in patterning the gastrula mesoderm. Two T-box transcription factors, Spadetail (Spt) and No tail (Ntl)/Brachyury are required to specify specific mesodermal cell types, and together, the two T-box genes are required for development of all trunk and tail mesoderm. To understand how Spt and Ntl mediate mesodermal cell fate decisions, we have identified putative target genes using zebrafish microarrays, and are investigating the expression and function of putative targets, as well as characterizing regulatory regions that control their T-box-regulated expression. Intriguingly, several of the putative targets encode “cyclic” genes, implicating Spt and Ntl as important upstream regulators of the segmentation clock, a dynamic molecular oscillator with a periodicity equal to that of somite formation.

Mesodermal segmentation. Following gastrulation, the trunk and tail mesoderm becomes segmented into a reiterated series of tissue blocks called somites. Somitogenesis is regulated both spatially and temporally and is controlled by the segmentation clock and by cell-cell interactions among presomitic cells. To uncover the molecular nature of the segmentation clock, we have performed genetic screens to identify and characterize mutations that disrupt cyclic gene expression. To understand how cyclic gene expression, thus segmentation clock function, is initiated, maintained, and eventually extinguished, we have constructed a transgenic line that allows us to follow oscillating gene expression in single cells in live wildtype and mutant embryos. Using this line, we are investigating the function of candidate regulators, like Spt and Ntl and their targets, in starting, stopping, and synchronizing the segmentation clock.

Cellular interactions during somitogenesis. In addition to studying the dynamic cell behaviors that occur prior to segmentation, we also use a variety of approaches to study somitic cell behaviors during and after segmentation. To understand mutant phenotypes, and thus gene function, at the level of single cells, we are using time-lapse microscopy of wild-type and mutant embryos to observe cell-cell contacts and interactions occurring before, during, and after somites form. In zebrafish, the majority of somitic cells form muscle, and we have discovered that a small population of early-differentiating slow muscle cells induces the morphogenesis of their fast muscle neighbors as they migrate through the somite to their final position. Currently, we are pursuing the molecular nature of the trigger.

Role of muscle-specific splicing in muscle function. In collaboration with the Conboy lab (LBNL), we have uncovered a critical role for RRM domain-containing Fox proteins in skeletal and cardiac muscle function. We have identified multiple genes with alternative exons whose splicing is altered in the absence of Fox function, and our knockdown experiments have shown that Fox-deficient embryos, although quite normal by morphology, are completely paralyzed and have irregular and slow heartbeat. We are currently focusing on uncovering how the Fox-regulated muscle-splicing program creates specific isoforms critical for function and physiology of muscle.

Selected Publications:

• • Morrow ZT, Maxwell AM, Hoshijima K, Talbot JC, Grunwald DJ, Amacher SL (2017) tbx6l and tbx16 are redundantly required for posterior paraxial mesoderm formation during zebrafish embryogenesis. Dev Dyn 246, 759-769. doi: 10.1002/dvdy.24547.

• • Gallagher TL, Tietz KT, Morrow ZT, McCammon JM, Goldrich ML, Derr NL, Amacher SL (2017) Pnrc2 regulates 3’UTR-mediated decay of segmentation clock-associated transcripts during zebrafish segmentation. Dev Biol 429, 225-239. doi: 10.1016/j.ydbio.2017.06.024.

• • Berberoglu MA, Gallagher TL, Morrow ZT, Talbot JC, Hromowyk KJ, Tenente IM, Langenau DM, Amacher SL (2017) Satellite-like cells contribute to pax7-dependent skeletal muscle repair in adult zebrafish. Dev Biol 424, 162-180. doi: 10.1016/j.ydbio.2017.03.004.

• • Li M, Hromowyk KJ, Amacher SL, Currie PD (2017) Muscular dystrophy modeling in zebrafish. Methods Cell Biol 138, 347-380. doi: 10.1016/bs.mcb.2016.11.004.

• • Martin BL, Gallagher TL, Rastogi N, Davis JP, Beattie CE, Amacher SL, Janssen PM (2015) In vivo assessment of contractile strength distinguishes differential gene function in skeletal muscle of zebrafish larvae. J Appl Physiol 119, 799-806. doi: 10.1152/japplphysiol.00447.2015.

• • Shih NP, François P, Delaune EA, Amacher SL (2015) Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity. Development 142, 1785-93. doi: 10.1242/dev.119057.

• • Talbot JC, Amacher SL (2014) A streamlined CRISPR pipeline to reliably generate zebrafish frameshifting alleles. Zebrafish 11, 583-5. doi: 10.1089/zeb.2014.1047.

• • Fior R, Maxwell AA, Ma TP, Vezzaro A, Moens CB, Amacher SL, Lewis J, Saúde L (2012) The differentiation and movement of presomitic mesoderm progenitor cells are controlled by Mesogenin 1. Development 139, 4656-65. doi: 10.1242/dev.078923.

• • Delaune EA, François P, Shih NP, Amacher SL (2012) Single-cell-resolution imaging of the impact of Notch signaling and mitosis on segmentation clock dynamics. Dev Cell 23, 995-1005. doi: 10.1016/j.devcel.2012.09.009.

• • Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 26, 702-8. doi: 10.1038/nbt1409.

• • Henry CA, Amacher SL (2004) Zebrafish slow muscle cell migration induces a wave of fast muscle morphogenesis. Dev Cell 7, 917-23.

NCBI link: https://www.ncbi.nlm.nih.gov/sites/myncbi/sharon.amacher.1/bibliography/40797248/public/?sort=date&direction=descending