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Structural basis for recognition of H3K56-acetylated histone H3–H4 by the chaperone Rtt106
Open accessAbstract
Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.
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“Rtt106, a fungal-specific histone chaperone, functions in histone deposition during DNA replication and transcription elongation in S. cerevisiae, and preferentially binds H3K56-acetylated histone H3-H424–26.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [24]
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Metadata
- Authors
- Su, D., Hu, Q., Li, Q., Thompson, J. R., Cui, G., Fazly, A., Davies, B. A., Botuyan, M. V., Zhang, Z., & Mer, G.
- Affiliations
- Mayo Clinic (US)
- Corresponding author
- Zhang, Zhiguo
- Mer, Georges
- ORCID
- Venue
- Nature
- Published
- 2012-02-05
- Volume
- 483
- Issue
- 7387
- Pages
- 104-107
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3439842
- OpenAlex
- W2046725709
- Cited by
- 128
- References
- 38
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 8 · 2023: 3 · 2022: 4 · 2021: 10 · 2020: 10 · 2019: 6 · 2018: 9 · 2017: 10 · 2016: 13 · 2015: 12 · 2014: 8 · 2013: 15 · 2012: 11
- FWCI
- 5.91
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Cancer Institute (P50CA108961, R01CA132878)
- National Institute of General Medical Sciences (R01GM072719)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- H3K56 acetylation, histone chaperone, nucleosome assembly, DNA replication, pleckstrin homology domain, histone acetylation, chromatin structure, Saccharomyces cerevisiae, histone deposition, conformational entropy
- MeSH terms
- Acetylation, Animals, Binding Sites, DNA Damage, Histones, Lysine, Models, Molecular, Mutation, Magnetic Resonance Spectroscopy, Protein Binding, Saccharomyces cerevisiae, Structure-Activity Relationship, Substrate Specificity, Xenopus laevis, Protein Structure, Tertiary, Crystallography, X-Ray, Pliability, Molecular Chaperones, Gene Silencing, Saccharomyces cerevisiae Proteins, Genomic Instability, Protein Multimerization
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