Gene syntax defines supercoiling-mediated transcriptional feedback

Science, vol. 392, pp. eadw1925

Abstract

Gene syntax-the order and arrangement of genes and their regulatory elements-shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that supercoiling-mediated feedback regulates expression of adjacent genes in a syntax-specific manner. Using Region Capture Micro-C, we measure induction-dependent formation of supercoiled plectonemes and syntax-specific chromatin structures in human induced pluripotent stem cells. Using syntax as a design parameter, we built compact gene circuits, tuning the mean, variance, and stoichiometries of expression across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

Authors 14

1. Kasey S. Love

   Massachusetts Institute of Technology

   Affiliation as printed

   Department of Biological Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Massachusetts Institute of Technology

2. Sneha R Kabaria

   Massachusetts Institute of Technology

   Affiliation as printed

   Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Massachusetts Institute of Technology

3. Ross D. Jones

   University of British Columbia

   Affiliation as printed

   Michael Smith Laboratories, UBC, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada

   School of Biomedical Engineering, UBC, 6088 University Boulevard, Vancouver, BC, V6T 1Z3, Canada

   University of British Columbia

4. Albert Blanch-Asensio Aachen

   Leiden University Medical Center · Massachusetts Institute of Technology

   Affiliation as printed

   Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Leiden University Medical Center

5. Deon S. Ploessl

   Massachusetts Institute of Technology

   Affiliation as printed

   Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Massachusetts Institute of Technology

6. Emma L. Peterman

   Massachusetts Institute of Technology

   Affiliation as printed

   Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Massachusetts Institute of Technology

7. Rachel Lee

   Massachusetts Institute of Technology

   Affiliation as printed

   Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

   Massachusetts Institute of Technology

8. Jiyoung Yun

   University of British Columbia

   Affiliation as printed

   Michael Smith Laboratories, UBC, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada

   School of Biomedical Engineering, UBC, 6088 University Boulevard, Vancouver, BC, V6T 1Z3, Canada

   University of British Columbia

9. Conrad G. Oakes

   California Institute of Technology

   Affiliation as printed

   Department of Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA

   California Institute of Technology

10. Christine L. Mummery Aachen Department of Anatomy and Embryology Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW)

    Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine

    Affiliation as printed

    Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands

    The Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Leiden University Medical Center

    Leiden University Medical Center

11. Richard P. Davis Aachen Department of Anatomy and Embryology Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW)

    Leiden University Medical Center · Novo Nordisk Foundation Center for Stem Cell Medicine

    Affiliation as printed

    Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands

    The Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Leiden University Medical Center

    Leiden University Medical Center

12. Brandon J. DeKosky

    Ragon Institute of MGH, MIT and Harvard · Massachusetts Institute of Technology

    Affiliation as printed

    Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

    The Ragon Institute of Mass General, MIT, and Harvard, 600 Main St., Cambridge, MA, 02139, USA

    Massachusetts Institute of Technology

13. Peter W. Zandstra

    University of British Columbia

    Affiliation as printed

    Michael Smith Laboratories, UBC, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada

    School of Biomedical Engineering, UBC, 6088 University Boulevard, Vancouver, BC, V6T 1Z3, Canada

    University of British Columbia

14. Kate E. Galloway corresponding

    Massachusetts Institute of Technology

    Affiliation as printed

    Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA

    Massachusetts Institute of Technology