Research Interests

We are interested in how cells become sequentially determined to more precisely defined fates during vertebrate embryonic development, and how this process depends upon cell position and upon interactions among neighboring cells. To address these questions, we use genetics, molecular biology, time-lapse imaging, and embryology to investigate muscle patterning and segmentation in the zebrafish embryo.

Current Projects

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 (30 minutes in the zebrafish).

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 muscle cells induces the morphogenesis of their 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 Rbfox RNA-binding proteins in skeletal and cardiac muscle function. We have identified multiple genes with alternative exons whose splicing is altered in the absence of Rbfox function, and our knockdown experiments have shown that Rbox-deficient embryos, although quite normal by morphology, are completely paralyzed and have irregular and slow heartbeat. We are currently focusing on uncovering how the Rbfox-regulated muscle-splicing program creates specific isoforms critical for function and physiology of muscle.

Selected Publications

• See a complete listing of Amacher's 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. Developmental dynamics 246, 759-769.
• 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. Developmental biology 429, 225-239.
• 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. Developmental biology 424, 162-180.
• Martin BL, Gallagher TL, Rastogi N, Davis JP, Beattie CB, Amacher SL, Janssen PM (2015) In vivo assessment of contractile strength distinguishes differential gene function in skeletal muscle of zebrafish larvae. Journal of Applied Physiology 119, 799-806.
• Shih NP, François P, Delaune EA, Amacher SL (2015) Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity. Development 142, 1785-1793.
• Talbot JC, Amacher SL (2014) A streamlined CRISPR pipeline to reliably generate zebrafish frameshifting alleles. Zebrafish 11, 583-585. Supplement.
• 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. Developmental Cell 23, 995-1005.
• Gallagher TL, Arribere JA, Geurts PA, Exner CR, McDonald KL, Dill KK, Marr HL, Adkar SS, Garnett AT, Amacher SL*, Conboy JG* (2011) Rbfox-regulated alternative splicing is critical for zebrafish cardiac and skeletal muscle functions. Developmental Biology 359, 251-261.
• Baskin JM, Dehnert KW, Laughlin ST, Amacher SL, Bertozzi CR (2010) Visualizing enveloping layer glycans during zebrafish early embryogenesis. PNAS 107, 10360-10365.
• Garnett AT, Han TM, Gilchrist MJ, Smith JC, Eisen MB, Wardle, FC, Amacher SL (2009) Identification of direct T-box target genes in the developing zebrafish mesoderm. Development 136, 749-760.
• Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah G, 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. Nature Biotechnology 26, 702-708.
• Laughlin ST, Baskin JM, Amacher SL, Bertozzi CR (2008) In vivo imaging of membrane-associated glycans in developing zebrafish. Science 320, 664-667.
• Daggett DF, Domingo CR, Currie PD, Amacher SL (2007) Control of morphogenetic cell movements in the early zebrafish myotome. Developmental Biology 309, 169-179.
• Henry CA, McNulty IM, Durst WA, Munchel SE, Amacher SL (2005) Interactions between muscle fibers and segment boundaries in zebrafish. Developmental Biology 287, 346-360.
• Dill KK, Amacher SL (2005) tortuga refines Notch pathway gene expression in the zebrafish presomitic mesoderm at the post-transcriptional level. Developmental Biology 287, 225-236.
• Henry CA, Amacher SL (2004) Zebrafish slow muscle cell migration induces a wave of fast muscle morphogenesis. Developmental Cell 7, 917-923.
• Henry CA, Urban MK, Dill KK, Merlie JP, Page MF, Kimmel CB, Amacher SL (2002) Two linked hairy/Enhancer of split-related zebrafish genes, her1 and her7, function together to refine alternating somite boundaries. Development 129, 3693-704.