Scott Aoki Lab

Projects

A. RNA recognition by binding proteins

We’re interested in how proteins recognize RNA, with a particular focus on RNA modifications. Can we develop new methods to identify and study RNA modifications? Where are the sites of understudied RNA modifications, and what are their biochemical and biological functions? The work has been and continues to be highly collaborative.

publications

  • Angelo M, Zhang W, Vilseck JZ, Aoki ST. In silico λ-dynamics predicts protein binding specificities to modified RNAs. bioRxiv [Preprint]. 2024 Jan 27:2024.01.26.577511. doi: 10.1101/2024.01.26.577511. PDF
    • First to use lambda dynamics to predict modified RNA-protein binding

B. Macromolecular RNA-protein complex assemblies and their biochemical functions

RNA-protein complexes can assemble into higher ordered structures, sometimes forming granules or biomolecular condensates. How do these granules assemble and what structural order is within these granules? How do other components assemble with core granule components? What are the biochemical functions of these granules? This investigation uses biochemistry and structural biology methods.

publications

  • Aoki ST, Crittenden S, Lynch T, Bingman CA, Wickens M, Kimble J. C. elegans germ granules require both assembly and localized regulators for mRNA repression. Nat Commun. 2021 Feb 12;12(1):996. PDF

C. Biological functions of RNA-protein complexes in situ

We’re interested in how proteins recognize RNA, with a particular focus on RNA modifications. Can we develop methods to track the stability and inheritance of RNA-protein complexes in model organisms? How does RNA-protein complex assembly connect to its inheritance and function in germ cells destined to become future progeny? The C. elegans germline continues to be our muse.

publications

  • Doenier J, Lynch TR, Kimble J, *Aoki ST. An improved in vivo tethering assay with single molecule FISH reveals that a nematode Nanos enhances reporter expression and mRNA stability. RNA. 2021 Jun;27(6):643-652. PDF
  • Aoki ST, Crittenden S, Lynch T, Bingman CA, Wickens M, Kimble J. C. elegans germ granules require both assembly and localized regulators for mRNA repression. Nat Commun. 2021 Feb 12;12(1):996. PDF

D. Identify and develop hidden science talent

An educational interest is discovering new strategies to recognize and nurture science talent in our community. How can we find science talent in our community? How can we effectively develop trainees for STEM careers?

publications

E. Miscellaneous

Collaborations and prior work before my independent career. Many thanks to Steve Harrison (PhD) and Judith Kimble (postdoc) for a stellar training experience and to all others I’ve worked with over the years.

publications

  • Aoki ST, Matreyek, KA. Practical Apps for a new lab. PLOS Blogs, ECR Community. 2/14/2020. https://ecrcommunity.plos.org/2020/02/14/practical-apps-for-a-new-lab/
  • Aoki ST, Porter DF, Prasad A, Wickens M, Bingman CA, Kimble J. An RNA-Binding Multimer Specifies Nematode Sperm Fate. Cell Rep. 2018 Jun 26;23(13):3769-3775. PDF
  • Aoki ST, Kershner A, Bingman CA, Wickens M, Kimble J. PGL germ granule assembly protein is a base-specific, single-stranded RNase.PNAS. 2016 Jan 19. PDF
  • Noble D, Aoki ST, Ortiz MA, Kim KW, Verheyden JM, Kimble J. Genomic Analyses of Sperm Fate Regulator Targets Reveal a Common Set of Oogenic mRNAs in Caenorhabditis elegans. Genetics. 2015 Nov 12. pii: genetics.115.182592. PDF
  • Wadford DA, Kauffman RC, Deere JD, Aoki ST, Stanton RA, Higgins J, Van Rompay KK, Villalobos A, Nettles JH, Schinazi RF, Pedersen NC, North TW. (2014) Variation of human immunodeficiency virus type-1 reverse transcriptase within the simian immunodeficiency virus genome of RT-SHIV. PLoS One. 2014 9. e86997. PDF
  • Wu F, Ourmanov I, Kuwata T, Goeken R, Brown CR, Buckler-White A, Iyengar R, Plishka R, Aoki ST, Hirsch VM. (2012) Sequential evolution and escape from neutralization of simian immunodeficiency virus SIVsmE660 clones in rhesus macaques. J Virol. 86, 8835-47. PDF
  • Aoki ST, Trask SD, Coulson BS, Greenberg HB, Dormitzer PR, Harrison SC. (2011) Cross-linking of rotavirus outer capsid protein VP7 by antibodies or disulfides inhibits viral entry. J Virol. 85, 10509-17. PDF
  • Aoki ST, Settembre EC, Trask SD, Greenberg HB, Harrison SC, Dormitzer PR. (2009) Structure of rotavirus outer-layer protein VP7 bound with a neutralizing Fab. Science. 324, 1444-7. PDF
  • Chen JZ, Settembre EC, Aoki ST, Zhang X, Bellamy AR, Dormitzer PR, Harrison SC, Grigorieff N. (2009) Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc Natl Acad Sci U S A. 106, 10644-8..01.26.577511. PDF

F. Funding

3Aug2024