Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
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.
Article and author information
Author details
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
- Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States
Version history
- Received: March 3, 2021
- Accepted: April 25, 2021
- Accepted Manuscript published: April 27, 2021 (version 1)
- Accepted Manuscript updated: April 30, 2021 (version 2)
- 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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Further reading
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- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push–pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
To find nucleosomes, chromatin remodelers slide and hop along DNA, and their direction of approach affects the direction that nucleosomes slide in.