The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Sheldrick, G. M. (2007) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767307043930 · Cited by 88,113
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., & Bax, A. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197809 · Cited by 15,961
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,723
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,796
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
MOLMOL: A program for display and analysis of macromolecular structures
Koradi, R., Billeter, M., & Wüthrich, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00009-4 · Cited by 7,156
PHENIX : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361
Automated protein model building combined with iterative structure refinement.
Perrakis, A., Morris, R. J., & Lamzin, V. S. (1999) · Nature Structural Biology · doi:10.1038/8263 · Cited by 2,423
Minor, W., Cymborowski, M., Otwinowski, Z., & Chruszcz, M. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906019949 · Cited by 2,097
The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification
Puig, Ó., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado‐Nilsson, E., Wilm, M. S., & Séraphin, B. (2001) · Methods · doi:10.1006/meth.2001.1183 · Cited by 1,784
Structure and ligand of a histone acetyltransferase bromodomain
Dhalluin, C., Carlson, J. E., Zeng, L., He, C., Aggarwal, A. K., Zhou, M.-M., & Zhou, M.-M. (1999) · Nature · doi:10.1038/20974 · Cited by 1,732
Elevated recombination rates in transcriptionally active DNA
Thomas, B. J., & Rothstein, R. J. (1989) · Cell · doi:10.1016/0092-8674(89)90584-9 · Cited by 1,603
Likelihood-enhanced fast rotation functions
Storoni, L. C., McCoy, A. J., & Read, R. J. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444903028956 · Cited by 1,177
Hendrickson, W. A., Horton, J. R., & LeMaster, D. M. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb08287.x · Cited by 1,015
Preparation of nucleosome core particle from recombinant histones
Luger, K., Rechsteiner, T. J., & Richmond, T. J. (1999) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(99)04003-3 · Cited by 779
CBP/p300-mediated acetylation of histone H3 on lysine 56
Das, C., Lucia, M. S., Hansen, K. C., & Tyler, J. K. (2009) · Nature · doi:10.1038/nature07861 · Cited by 698
SOLVE and RESOLVE: Automated Structure Solution and Density Modification
Terwilliger, T. C. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)74002-6 · Cited by 466
Acetylation of Histone H3 Lysine 56 Regulates Replication-Coupled Nucleosome Assembly
Li, Q., Zhou, H., Wurtele, H., Davies, B., Horazdovsky, B., Verreault, A., & Zhang, Z. (2008) · Cell · doi:10.1016/j.cell.2008.06.018 · Cited by 447
Self-citationChen, C., Carson, J. J., Feser, J., Tamburini, B. A. J., Zabaronick, S., Linger, J. G., & Tyler, J. K. (2008) · Cell · doi:10.1016/j.cell.2008.06.035 · Cited by 426
White, C. L., Suto, R. K., & Luger, K. (2001) · The EMBO Journal · doi:10.1093/emboj/20.18.5207 · Cited by 420
Screen for DNA‐damage‐responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells
Tjeertes, J. V., Miller, K. M., & Jackson, S. P. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.119 · Cited by 347
Histone H3-K56 acetylation is important for genomic stability in mammals
Yuan, J., Pu, M., Zhang, Z., & Lou, Z. (2009) · Cell Cycle · doi:10.4161/cc.8.11.8620 · Cited by 254
Self-citationNMR spectroscopy: a multifaceted approach to macromolecular structure
Ferentz, A. E., & Wagner, G. (2000) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583500003589 · Cited by 239
Williams, S. K., Truong, D. M., & Tyler, J. K. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800057105 · Cited by 229
Xie, W., Song, C., Young, N. L., Sperling, A. S., Xu, F., Sridharan, R., Conway, A. E., Garcia, B. A., Plath, K., Clark, A. T., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.004 · Cited by 197
Luger, K. (2006) · Chromosome Research · doi:10.1007/s10577-005-1026-1 · Cited by 172
The PH superfold: a structural scaffold for multiple functions
Blomberg, N., Baraldi, E., Nilges, M., & Saraste, M. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(99)01472-3 · Cited by 166
Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information
Corpet, A., & Almouzni, G. (2008) · Trends in Cell Biology · doi:10.1016/j.tcb.2008.10.002 · Cited by 157
VanDemark, A. P., Blanksma, M. C., Ferris, E., Heroux, A., Hill, C. P., & Formosa, T. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.03.025 · Cited by 144
Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing
Huang, S., Zhou, H., Katzmann, D., Hochstrasser, M., Atanasova, E., & Zhang, Z. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506176102 · Cited by 130
Self-citationHuang, R., Holbert, M. A., Tarrant, M. K., Curtet, S., Colquhoun, D. R., Rabbitts, B. M., Dancy, B. C. R., Hwang, Y., Tang, Y., Meeth, K. M., et al. (2010) · Journal of the American Chemical Society · doi:10.1021/ja103954u · Cited by 116
Bowman, A. J., Ward, R., Mkami, H. E., Owen‐Hughes, T., & Norman, D. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1003 · Cited by 105
Structural Basis of BACH1 Phosphopeptide Recognition by BRCA1 Tandem BRCT Domains
Botuyan, M. V., Nominé, Y., Yu, X., Juranić, N., Macura, S. I., Chen, J., & Mer, G. (2004) · Structure · doi:10.1016/j.str.2004.06.002 · Cited by 95
Self-citationA novel role for histone chaperones CAF‐1 and Rtt106p in heterochromatin silencing
Huang, S., Zhou, H., Tarara, J., & Zhang, Z. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601670 · Cited by 77
Self-citationZhou, H., Madden, B. J., Muddiman, D. C., & Zhang, Z. (2006) · Biochemistry · doi:10.1021/bi0521083 · Cited by 73
Self-citationStructural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing
Liu, Y., Huang, H., Zhou, B. O., Wang, S., Hu, Y., Li, X., Liu, J., Zang, J., Niu, L., Wu, J., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.055996 · Cited by 39
Flagged first, then by citations
Cited by
Sorted by citations
Histone core modifications regulating nucleosome structure and dynamics
Tessarz, P., & Kouzarides, T. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3890 · Cited by 1,018
Histone exchange, chromatin structure and the regulation of transcription
Venkatesh, S., & Workman, J. L. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3941 · Cited by 997
Perceiving the epigenetic landscape through histone readers
Musselman, C. A., Lalonde, M., Côté, J., & Kutateladze, T. G. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2436 · Cited by 897
Histone chaperone networks shaping chromatin function
Hammond, C. M., Strømme, C. B., Huang, H., Patel, D. J., & Groth, A. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.159 · Cited by 539
Post-Translational Modifications of Histones That Influence Nucleosome Dynamics
Bowman, G. D., & Poirier, M. G. (2014) · Chemical Reviews · doi:10.1021/cr500350x · Cited by 549
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
