1. Chromosomes and Gene Expression
  2. Computational and Systems Biology
Download icon

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
Research Article
  • Cited 0
  • Views 620
  • Annotations
Cite this article as: eLife 2021;10:e68068 doi: 10.7554/eLife.68068
Voice your concerns about research culture and research communication: Have your say in our 7th annual survey.

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

    Department of Computer Science, 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 Structural Biology, 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 Structural Biology, 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)

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.

Metrics

  • 620
    Page views
  • 147
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Cancer Biology
    2. Chromosomes and Gene Expression
    Carter J Barger et al.
    Research Article Updated

    The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co-expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers.

    1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease
    J Stephan Wichers et al.
    Research Article Updated

    Sequestration of Plasmodium falciparum(P. falciparum)-infected erythrocytes to host endothelium through the parasite-derived P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion proteins is central to the development of malaria pathogenesis. PfEMP1 proteins have diversified and expanded to encompass many sequence variants, conferring each parasite a similar array of human endothelial receptor-binding phenotypes. Here, we analyzed RNA-seq profiles of parasites isolated from 32 P. falciparum-infected adult travellers returning to Germany. Patients were categorized into either malaria naive (n = 15) or pre-exposed (n = 17), and into severe (n = 8) or non-severe (n = 24) cases. For differential expression analysis, PfEMP1-encoding var gene transcripts were de novo assembled from RNA-seq data and, in parallel, var-expressed sequence tags were analyzed and used to predict the encoded domain composition of the transcripts. Both approaches showed in concordance that severe malaria was associated with PfEMP1 containing the endothelial protein C receptor (EPCR)-binding CIDRα1 domain, whereas CD36-binding PfEMP1 was linked to non-severe malaria outcomes. First-time infected adults were more likely to develop severe symptoms and tended to be infected for a longer period. Thus, parasites with more pathogenic PfEMP1 variants are more common in patients with a naive immune status, and/or adverse inflammatory host responses to first infections favor the growth of EPCR-binding parasites.