Possible Rotation Projects:
- Mechanisms driving de novo gene activation in the embryo
- Molecular determinants of RNA regulation during development
- Comparative genomics of pluripotency induction across vertebrates
Training Technologies Used:
- Genomics, e.g. RNA-seq, ChIP-seq; Genetic engineering, e,g. CRISPR/Cas; Embryology, e.g. zebrafish microinjection; Molecular biology; Bioinformatic analysis and methods development.
- B.S. Symbolic Systems, Stanford University, 2000
- M.S. Computer Science, Stanford University, 2002
- Ph.D. Genomics and Computational Biology, University of Pennsylvania, 2009
Hurton MD, Miller JM, Lee MT. 2025. H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition. PLOS Biology 23(7): e3003239.
Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT. 2023. Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis. eLife 12: e83952.
Ayers TN, Nicotra ML, Lee MT. 2023. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLOS Genetics 19(7): e1010845. (Cover)
Blatt P, Wong-Deyrup SW, McCarthy A, Breznak S, Hurton MD, Upadhyay M, Bennink B, Camacho J, Lee MT‡, Rangan P‡. 2021. RNA degradation is required for the germ-cell to maternal transition in Drosophila. Current Biology 31(14), 2984-2994.e7. ‡ Co-corresponding authors.
Phelps W, Carlson AE, Lee MT. 2021. Optimized design of tiled antisense oligos for targeted RNA depletion. Nucleic Acids Res 49(1): e5.
Yartseva V, Takacs CM, Vejnar CE, Lee MT‡, Giraldez AG‡. 2017. RESA identifies mRNA regulatory sequences with high resolution. Nature Methods 14, 201-207. ‡ Co-corresponding authors.
Lee MT#, Bonneau AR#, Giraldez AJ‡. Zygotic genome activation during the maternal-to-zygotic transition. 2014. Annu Rev Cell Dev Biol 30(1), 18.1-18.33. # Co-lead authors, ‡ Co-corresponding authors.
Lee MT#, Bonneau AR#, Takacs CM, Bazzini AB, DiVito KR, Fleming ES, Giraldez AJ. 2013. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 503(7476), 360-364. # Co-lead authors.
Bazzini AA#, Lee MT#, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078), 233-237. # Co-lead authors.
How does a fertilized egg know how to develop? For most animals and plants, the genetic instructions that guide early embryogenesis are inherited as RNA. During a short window of development, these RNA coordinate all cellular activity, including the processes that induce the first rounds of transcription from the embryonic genome. Eventually those maternally inherited RNA are destroyed, as newly transcribed embryonic RNA assume control of the embryo. This period of development is called the maternal-to-zygotic transition.
Maternally inherited RNA encode the instructions to reprogram an egg into pluripotent embryonic stem cells, the precursors to all cell types in the adult organism. We study eggs, embryos, and their RNA and genomes to better understand the mechanisms underlying cellular identity and pluripotency, and how they have evolved. Our tool kit includes genetics, embryology, and high-throughput experimental and computational genomics across animals, including (so far) zebrafish, Xenopus, and the cnidarian Hydractinia symbiolongicarpus.
