Research Summary

The Floor Lab studies the control of gene expression at the level of RNA. DEAD-box RNA chaperones are a major focus of the lab, which remodel RNA structures and RNA-protein interactions. Some questions we’re interested in are: how do DEAD-box proteins influence RNA structure and bound proteins in cells? How do these changes affect cell state? Do DEAD-box proteins act as molecular dispersants for RNA? How can we measure translation and protein binding on single RNA molecules in cells? We use diverse deep sequencing approaches, biochemistry, imaging, computational analysis, and develop new methods to answer these questions.

Research Funding

  • January 1, 2021 - November 30, 2025 - Cellular and molecular mechanisms underlying DDX3X syndrome , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01NS120667
  • September 30, 2018 - May 31, 2023 - The impact of human RNA diversity on protein production and cell fate , Principal Investigator . Sponsor: NIH, Sponsor Award ID: DP2GM132932
  • April 1, 2018 - March 31, 2021 - Oncogenic reprogramming of protein translation by DDX3 inactivation , Principal Investigator . Sponsor: California Tobacco Related Disease Research Program, Sponsor Award ID: 27KT-0003

Education

University of Kansas, Lawrence, Kansas, Bachelor of Science, 05/2005, Computer Science
University of Kansas, Lawrence, Kansas, Bachelor of Science, 05/2005, Physics
University of California, San Francisco, Doctor of Philosophy, 09/2011, Biophysics
University of California, Berkeley, Postdoctoral Fellow, 2017, Molecular and Cell Biology

Honors & Awards

  • 2004
    Barry M. Goldwater Scholar, The Barry Goldwater Scholarship and Excellence in Education Foundation
  • 2007
    Achievement Rewards for College Scientists Scholar, ARCS Foundation
  • 2007
    Genentech-Sandler Graduate Research Opportunity Fellow, UCSF
  • 2009
    Mel Jones Award for College Scientists Scholar, ARCS Foundation
  • 2010
    Achievement Rewards for College Scientists Scholar, ARCS Foundation
  • 2011
    Frank M. Goyan Award for Outstanding Physical Chemistry Thesis, UCSF
  • 2013
    Helen Hay Whitney Foundation Postdoctoral Fellow, Helen Hay Whitney Foundation

Selected Publications

  1. Wilkins KC, Schroeder T, Gu S, Revalde JL, Floor SN. Determinants of DDX3X sensitivity uncovered using a helicase activity in translation reporter. bioRxiv. 2023 Sep 14.  View on PubMed
  2. Lin Y, Floor SN. Dynamic regulation of messenger RNA structure controls translation. Nature. 2023 Sep; 621(7978):259-260.  View on PubMed
  3. Gadek M, Sherr EH, Floor SN. The variant landscape and function of DDX3X in cancer and neurodevelopmental disorders. Trends Mol Med. 2023 09; 29(9):726-739.  View on PubMed
  4. Campbell AE, Dyle MC, Albanese R, Matheny T, Sudheendran K, Cortázar MA, Forman T, Fu R, Gillen AE, Caruthers MH, Floor SN, Calviello L, Jagannathan S. Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression. Cell Rep. 2023 Jun 13; 42(6):112642.  View on PubMed
  5. Jowhar Z, Xu A, Venkataramanan S, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. bioRxiv. 2023 May 12.  View on PubMed
  6. Hoye ML, Calviello L, Poff AJ, Ejimogu NE, Newman CR, Montgomery MD, Ou J, Floor SN, Silver DL. Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model. Elife. 2022 06 28; 11.  View on PubMed
  7. Wilkins KC, Venkataramanan S, Floor SN. Lysate and cell-based assays to probe the translational role of RNA helicases. Methods Enzymol. 2022; 673:141-168.  View on PubMed
  8. Yu T, Cazares O, Tang AD, Kim HY, Wald T, Verma A, Liu Q, Barcellos-Hoff MH, Floor SN, Jung HS, Brooks AN, Klein OD. SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal. Dev Cell. 2022 03 14; 57(5):624-637.e4.  View on PubMed
  9. Jesslyn Park, Srivats Venkataramanan, José Liboy-Lugo, Virginia K. Blackwell, Stephen N. Floor. Determining the impact of stress granule composition on cell survival. Biophysical Journal. 2022 Feb 1; 121(3):210a.  View on PubMed
  10. Jessica Sheu-Gruttadauria, Xiaowei Yan, Nico Stuurman, Stephen Floor, Ronald D. Vale. Mapping the regulatory landscape of membraneless organelle assembly and dynamics. Biophysical Journal. 2022 Feb 1; 121(3):293a-294a.  View on PubMed
  11. Angela L. Gao, Jose Liboy-Lugo, Jesslyn Park, Stephen N. Floor. The impact of periodic stress on stress granules in human cells. Biophysical Journal. 2022 Feb 1; 121(3):211a.  View on PubMed
  12. Jose Liboy-Lugo, Jessica Sheu-Gruttadauria, Stephen N. Floor. The role of G3BP stress granules assembly in cell fitness during the integrated stress response. Biophysical Journal. 2022 Feb 1; 121(3):497a.  View on PubMed
  13. Tsai K, Stojkovic V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. Elife. 2022 01 11; 11.  View on PubMed
  14. Venkataramanan S, Gadek M, Calviello L, Wilkins K, Floor SN. DDX3X and DDX3Y are redundant in protein synthesis. RNA. 2021 12; 27(12):1577-1588.  View on PubMed
  15. Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN. DDX3 depletion represses translation of mRNAs with complex 5' UTRs. Nucleic Acids Res. 2021 05 21; 49(9):5336-5350.  View on PubMed
  16. Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A. Control of ribosomal protein synthesis by the Microprocessor complex. Sci Signal. 2021 02 23; 14(671).  View on PubMed
  17. Chen M, Asanuma M, Takahashi M, Shichino Y, Mito M, Fujiwara K, Saito H, Floor SN, Ingolia NT, Sodeoka M, Dodo K, Ito T, Iwasaki S. Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A. Cell Chem Biol. 2021 04 15; 28(4):475-486.e8.  View on PubMed
  18. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468.  View on PubMed
  19. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22.  View on PubMed
  20. Lennox AL, Hoye ML, Jiang R, Johnson-Kerner BL, Suit LA, Venkataramanan S, Sheehan CJ, Alsina FC, Fregeau B, Aldinger KA, Moey C, Lobach I, Afenjar A, Babovic-Vuksanovic D, Bézieau S, Blackburn PR, Bunt J, Burglen L, Campeau PM, Charles P, Chung BHY, Cogné B, Curry C, D'Agostino MD, Di Donato N, Faivre L, Héron D, Innes AM, Isidor B, Keren B, Kimball A, Klee EW, Kuentz P, Küry S, Martin-Coignard D, Mirzaa G, Mignot C, Miyake N, Matsumoto N, Fujita A, Nava C, Nizon M, Rodriguez D, Blok LS, Thauvin-Robinet C, Thevenon J, Vincent M, Ziegler A, Dobyns W, Richards LJ, Barkovich AJ, Floor SN, Silver DL, Sherr EH. Pathogenic DDX3X Mutations Impair RNA Metabolism and Neurogenesis during Fetal Cortical Development. Neuron. 2020 05 06; 106(3):404-420.e8.  View on PubMed

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