Structure and flexibility of the yeast NuA4 histone acetyltransferase complex

Zukin, Stefan A; Marunde, Matthew R; Popova, Irina K; Soczek, Katarzyna M; Nogales, Eva; Patel, Avinash B

doi:10.7554/elife.81400

Cited by 23Genomics and Chromatin DynamicsChromatin Remodeling and CancerNuclear Structure and Function

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Structure and flexibility of the yeast NuA4 histone acetyltransferase complex

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Zukin, Stefan A, Marunde, Matthew R, Popova, Irina K, Soczek, Katarzyna M, Nogales, Eva, Patel, Avinash B·2022·eLife

DOI 10.7554/elife.81400PMC PMC9643008

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Abstract

The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.

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Authors: Zukin, S. A., Marunde, M. R., Popova, I. K., Soczek, K. M., Nogales, E., & Patel, A. B.
Affiliations: University of California, Berkeley (US)
EpiCypher (United States) (US)
Innovative Genomics Institute (US)
Howard Hughes Medical Institute (US)
Corresponding author: Nogales, Eva
Patel, Avinash B
ORCID: Zukin, Stefan A
Marunde, Matthew R
Popova, Irina K
Soczek, Katarzyna M
Nogales, Eva
Patel, Avinash B
Venue: eLife
Publisher: eLife Sciences Publications, Ltd
Published: 2022-10-20
Volume: 11
ISSN: 2050-084X (ISSN-L)
DOI: 10.7554/elife.81400
PMC: PMC9643008
OpenAlex: W4306871076
Cited by: 22
References: 112
Citations by year: 2025: 6 · 2024: 9 · 2023: 6 · 2022: 1
FWCI: 1.80
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/publicdomain/zero/1.0/ (vor)
creativecommons.org/publicdomain/zero/1.0/ (am)
creativecommons.org/publicdomain/zero/1.0/ (tdm)
Locations: eLife (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, public-domain)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eScholarship (California Digital Library) (submittedVersion, public-domain)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders: National Institute of General Medical Sciences (R35-GM127018, R44GM117683, R44GM116584)
Howard Hughes Medical Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords: histone H4 acetylation, histone H3K4me3, Tra1, Arp4, nucleosome recognition, nucleosome acetylation, transcriptional activation, DNA repair, Saccharomyces cerevisiae, protein complex structure, protein flexibility
MeSH terms: Acetylation, Nucleosomes, Saccharomyces cerevisiae, Cryoelectron Microscopy, Saccharomyces cerevisiae Proteins, Histone Acetyltransferases

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Structure and flexibility of the yeast NuA4 histone acetyltransferase complex

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