Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

  1. Adrian L Sanborn  Is a corresponding author
  2. Benjamin T Yeh
  3. Jordan T Feigerle
  4. Cynthia V Hao
  5. Raphael J L Townshend
  6. Erez Lieberman-Aiden
  7. Ron O Dror
  8. Roger D Kornberg  Is a corresponding author
  1. Stanford University, United States
  2. Baylor College of Medicine, United States
  3. Stanford University School of Medicine, United States

Abstract

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity ('fuzzy' binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

Data availability

All data from in vivo activation and in vitro screens are included in tables as source data files. PDB files of structural models of Med15-AD interactions are included in Figure 6-source data 2. All sequencing data have been deposited in GEO, under the accession code GSE173156.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Adrian L Sanborn

    Department of Structural Biology, Department of Computer Science, Stanford University, Stanford, United States
    For correspondence
    a@adriansanborn.com
    Competing interests
    The authors declare that no competing interests exist.
  2. Benjamin T Yeh

    David Geffen School of Medicine, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9397-6392
  3. Jordan T Feigerle

    Department of Molecular Physiology and Biophysics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Cynthia V Hao

    Department of Structural Biology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2183-0698
  5. Raphael J L Townshend

    Department of Computer Science, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Erez Lieberman-Aiden

    Baylor College of Medicine, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Ron O Dror

    Department of Computer Science, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Roger D Kornberg

    Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
    For correspondence
    kornberg@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2425-7519

Funding

National Institutes of Health (R01-DK121366 and R01-AI021144)

  • Roger D Kornberg

U.S. Department of Energy (Office of Science Graduate Student Research (SCGSR) program (DE-SC0014664))

  • Raphael J L Townshend

National Institutes of Health (F32-GM126704)

  • Jordan T Feigerle

National Institutes of Health (R01-GM127359)

  • Ron O Dror

U.S. Department of Energy (Scientific Discovery through Advanced Computing (SciDAC) program)

  • Ron O Dror

National Science Foundation (Physics Frontiers Center Award (PHY1427654))

  • Erez Lieberman-Aiden

Welch Foundation (Q-1866)

  • Erez Lieberman-Aiden

U.S. Department of Agriculture (Agriculture and Food Research Initiative Grant (2017-05741))

  • Erez Lieberman-Aiden

National Institutes of Health (4D Nucleome Grant (U01HL130010))

  • Erez Lieberman-Aiden

National Institutes of Health (Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375))

  • Erez Lieberman-Aiden

U.S. Department of Defense (National Defense Science & Engineering Graduate (NDSEG) Fellowship)

  • Adrian L Sanborn

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Publication history

  1. Received: March 3, 2021
  2. Accepted: April 25, 2021
  3. Accepted Manuscript published: April 27, 2021 (version 1)
  4. Accepted Manuscript updated: April 30, 2021 (version 2)
  5. Version of Record published: May 20, 2021 (version 3)

Copyright

© 2021, Sanborn et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Adrian L Sanborn
  2. Benjamin T Yeh
  3. Jordan T Feigerle
  4. Cynthia V Hao
  5. Raphael J L Townshend
  6. Erez Lieberman-Aiden
  7. Ron O Dror
  8. Roger D Kornberg
(2021)
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
eLife 10:e68068.
https://doi.org/10.7554/eLife.68068

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