James Gagnon

Assistant Professor of Biological Sciences

Gagnon Photo

B.S. Worcester Polytechnic Institute

Ph.D. Brown University

Research

References

james.gagnon@utah.edu

James Gagnon's Lab Page

James Gagnon's PubMed Literature Search

James Gagnon's Google Scholar

Molecular Biology Program

Developmental Biology, Genetics, Genomics

Research

Our lab tries to understand vertebrate embryogenesis and adult tissue homeostasis through the lens of the lineage tree. The lineage tree is the branching structure of cell divisions that describes relationships between all cells in the adult animal, and connects these cells to their ancestor cells in the embryo. We have developed tools to record this lineage tree, with unprecedented scale and granularity, using genome editing and sequencing.

Our lab studies variability in the vertebrate lineage tree - how it is compensated for and how it can lead to individuality. Our lab is interested in cell signaling pathways, and how they influence cell fate choice at critical branch points within the tree. Finally, our lab researches how stem cells contribute to tissue maintenance and regeneration, particularly in the blood and in the germ line. Our lab addresses these topics using genome engineering, sequencing and synthetic biology in the zebrafish, a great model of vertebrate biology.

References

Selected Publications

  1. Raj B, Wagner DW, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA*, Schier AF*. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nature Biotechnology 2018 36:442-450 PMID: 29608178
  2.  Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extra-embryonic tissue. Development 2018 145:dev147793 PMID: 29180571
  3. McKenna A*, Findlay G*, Gagnon JA*, Horwitz M, Schier AF, Shendure J. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science 2016 353:aaf7907 PMID: 27229144
  4. Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.PLoS One 2014 9:e98186 PMID: 24873830
  5. Montague TG*, Cruz JM*, Gagnon JA, Church GM, Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014 42:W401-7 PMID: 24861617
  6. Gagnon JA, Kreiling JA, Powrie EA, Wood TR, Mowry KL. Directional transport is mediated by a Dynein-dependent step in an RNA localization pathway. PLoS Biol. 2013 11:e1001551 PMID: 23637574

* Equal contribution

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Last Updated: 12/7/18