Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
- Stanford University, United States
- Baylor College of Medicine, United States
- 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.
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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Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
eLife 10:e68068.
https://doi.org/10.7554/eLife.68068
Further reading
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- Chromosomes and Gene Expression
The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here, we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
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- Chromosomes and Gene Expression
Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1’s association with two large hook-shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latter’s replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1’s N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the 20 years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1’s NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapl’s C-terminal domain. AF also reveals how Scc1’s dissociation from Smc3 arises from a distortion of Smc3’s CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.
