University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Stephen Floor, PhD

Stephen Floor, PhD

Assistant Professor, Dept. of Cell and Tissue Biology, UCSF

Cancer Center Program Memberships

Pediatric Malignancies

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.

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


Professional Experience

  • 2000-2001
    Undergraduate Research Assistant, University of Kansas, Physics Department
  • 2002-2004
    Undergraduate Research Assistant, University of Kansas, Physics Department
  • 2004-2004
    Undergraduate Research Assistant, University of Michigan, Physics Department
  • 2005-2011
    Graduate Research Assistant, UCSF, Biophysics Graduate Group
  • 2011-2017
    Postdoctoral Fellow, University of California, Berkeley, Dept. of Molecular and Cell Biology
  • 2017-present
    Assistant Professor, Dept. of Cell and Tissue Biology, UCSF

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. Arake de Tacca LM, Pulos-Holmes MC, Floor SN, Cate JHD. PTBP1 mRNA isoforms and regulation of their translation. RNA. 2019 Oct; 25(10):1324-1336.
    View on PubMed
  2. 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
  3. 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
  4. Venkataramanan S, Floor SN. The Traffic Jam: Polyamine Prevalence Pauses Protein Production. Mol Cell. 2018 04 19; 70(2):191-192.
    View on PubMed
  5. Thai B, Floor SN. Move Over, Genomes: Here Comes Transcriptome Engineering. CRISPR J. 2018 04; 1:126-127.
    View on PubMed
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. Elife. 2016 Jan 06; 5.
    View on PubMed
  13. 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
  14. 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
  15. Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3. J Biol Chem. 2016 Jan 29; 291(5):2412-21.
    View on PubMed
  16. Kendall Condon, Stephen Floor, Jennifer Doudna. Engineering Inhibitor Specificity in the Dead-Box Protein Family. Biophysical Journal. 2014 Jan 1; 106(2):495a-496a.
    View on PubMed
  17. Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure. 2013 Sep 03; 21(9):1571-80.
    View on PubMed
  18. Floor SN, Borja MS, Gross JD. Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2872-7.
    View on PubMed
  19. Floor SN, Jones BN, Hernandez GA, Gross JD. A split active site couples cap recognition by Dcp2 to activation. Nat Struct Mol Biol. 2010 Sep; 17(9):1096-101.
    View on PubMed
  20. Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR. Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid (13)C-p-methoxyphenylalanine. J Am Chem Soc. 2008 Dec 03; 130(48):16168-9.
    View on PubMed

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