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

  • September 30, 2018 - May 31, 2023 - The impact of human RNA diversity on protein production and cell fate, Principal Investigator. Sponsor: NIH/NIGMS, 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
  • September 30, 2018 - May 31, 2023 - The impact of human RNA diversity on protein production and cell fate, Principal Investigator. Sponsor: NIH/NIGMS, 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. 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
  2. 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 Feb 23; 14(671).  View on PubMed
  3. 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
  4. 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
  5. 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
  6. 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
  7. Arake de Tacca LM, Pulos-Holmes MC, Floor SN, Cate JHD. PTBP1 mRNA isoforms and regulation of their translation. RNA. 2019 10; 25(10):1324-1336.  View on PubMed
  8. Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, Ingolia NT. The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Mol Cell. 2019 02 21; 73(4):738-748.e9.  View on PubMed
  9. Richardson CD, Kazane KR, Feng SJ, Zelin E, Bray NL, Schäfer AJ, Floor SN, Corn JE. CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat Genet. 2018 08; 50(8):1132-1139.  View on PubMed
  10. Venkataramanan S, Floor SN. The Traffic Jam: Polyamine Prevalence Pauses Protein Production. Mol Cell. 2018 04 19; 70(2):191-192.  View on PubMed
  11. Thai B, Floor SN. Move Over, Genomes: Here Comes Transcriptome Engineering. CRISPR J. 2018 04; 1:126-127.  View on PubMed
  12. Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Rep. 2017 Nov 14; 21(7):2005-2016.  View on PubMed
  13. John D Blair, Dirk Hockemeyer, Jennifer A Doudna, Helen S Bateup, Stephen N Floor. Widespread translational remodeling during human neuronal differentiation. bioRxiv preprint. 2017.  View on PubMed
  14. Chris D. Richardson, Katelynn R. Kazane, Sharon J. Feng, Nicholas L. Bray, Axel J. Schaefer, Stephen Floor, Jacob Corn. CRISPR-Cas9 Genome Editing In Human Cells Works Via The Fanconi Anemia Pathway. bioRxiv preprint. 2017.  View on PubMed
  15. Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A, Doudna JA. Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes. Nat Biotechnol. 2017 05; 35(5):431-434.  View on PubMed
  16. Iwasaki S, Floor SN, Ingolia NT. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature. 2016 06 23; 534(7608):558-61.  View on PubMed
  17. Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget. 2016 May 10; 7(19):28169-82.  View on PubMed
  18. Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. Elife. 2016 Jan 06; 5.  View on PubMed
  19. Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA. Analog sensitive chemical inhibition of the DEAD-box protein DDX3. Protein Sci. 2016 Mar; 25(3):638-49.  View on PubMed
  20. Floor SN, Doudna JA. Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome. Mol Cell. 2015 Dec 03; 60(5):712-714.  View on PubMed

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