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Acetylation of Histone H3 Lysine 56 Regulates Replication-Coupled Nucleosome Assembly
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Chromatin assembly factor 1 (CAF-1) and Rtt106 participate in the deposition of newly synthesized histones onto replicating DNA to form nucleosomes. This process is critical for the maintenance of genome stability and inheritance of functionally specialized chromatin structures in proliferating cells. However, the molecular functions of the acetylation of newly synthesized histones in this DNA replication-coupled nucleosome assembly pathway remain enigmatic. Here we show that histone H3 acetylated at lysine 56 (H3K56Ac) is incorporated onto replicating DNA and, by increasing the binding affinity of CAF-1 and Rtt106 for histone H3, H3K56Ac enhances the ability of these histone chaperones to assemble DNA into nucleosomes. Genetic analysis indicates that H3K56Ac acts in a nonredundant manner with the acetylation of the N-terminal residues of H3 and H4 in nucleosome assembly. These results reveal a mechanism by which H3K56Ac regulates replication-coupled nucleosome assembly mediated by CAF-1 and Rtt106.
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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 [25]
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“Msh2-Msh6 is coupled to the moving replication fork via its interaction with PCNA (Kleczkowska et al. 2001; Hombauer et al. 2011a; Haye and Gammie 2015).”
BackgroundInfluentialSauer, P. V., Gu, Y., Liu, W. H., Mattiroli, F., Panne, D., Luger, K., & Churchill, M. E. A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky823 · Cited by 91
Liu, W. H., Roemer, S. C., Port, A. M., & Churchill, M. E. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks906 · Cited by 91
“In fact, biochemical analyses suggest that the Cac1 subunit of CAF-1 preferentially interacts withH3/H4 that has been acetylated on lysine 56 ofH3 (31).”
BackgroundH3–H4 Histone Chaperone Pathways
Grover, P., Asa, J. S., & Campos, E. I. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120417-031547 · Cited by 91
Histone H3 Lysine 56 Acetylation and the Response to DNA Replication Fork Damage
Würtele, H., Kaiser, G. S., Bacal, J., St-Hilaire, E., Lee, E. H., Tsao, S., Dorn, J. F., Maddox, P. S., Lisby, M., Pasero, P., et al. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05415-11 · Cited by 93
“to genotoxic agents than chromatin assembly mutants (41).”
BackgroundInfluentialSelf-citationBen-Shahar, T. R., Castillo, A. G., Osborne, M. J., Borden, K. L. B., Kornblatt, J. A., & Verreault, A. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01051-09 · Cited by 93
Self-citationHistone chaperone ASF1A is required for maintenance of pluripotency and cellular reprogramming
González-Muñoz, E., Arboleda-Estudillo, Y., Otu, H. H., & Cibelli, J. B. (2014) · Science · doi:10.1126/science.1254745 · Cited by 88
Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress
García‐Rodríguez, N., Wong, R. P. C., & Ulrich, H. D. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00087 · Cited by 90
“This in turn weakens H3 interaction with Asf1 and instead facilitates association with CAF-1 for subsequent deposition behind the replication fork.”
BackgroundInfluentialKari, V., Shchebet, A., Neumann, H., & Johnsen, S. A. (2011) · Cell Cycle · doi:10.4161/cc.10.20.17769 · Cited by 90
Histone chaperones link histone nuclear import and chromatin assembly
Keck, K. M., & Pemberton, L. F. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.09.007 · Cited by 87
Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition
Winkler, D. D., Zhou, H., Dar, M. A., Zhang, Z., & Luger, K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks812 · Cited by 88
“To perform sequential immunoprecipitation, we first purified Cac2-TAP using IgG sepharose following a standard procedure (16,31).”
BackgroundMethodInfluentialSelf-citationRetractedKebede, A. F., Schneider, R., & Daujat, S. (2014) · FEBS Journal · doi:10.1111/febs.13047 · Cited by 89
Clemente‐Ruiz, M., González‐Prieto, R., & Prado, F. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002376 · Cited by 86
“Indeed, Asf1 interacts with MCM [10] and with RFC – which loads PCNA and in this way replaces Pola with Pole and Pold – [8], and H3K56 acetylation regulates the function of the RFC [73]; it is thereby possible that the absence of Asf1 and/ or H3K56ac could specifically alter the distribution of the polymerases and the…”
BackgroundInfluentialThe Histone Chaperones Nap1 and Vps75 Bind Histones H3 and H4 in a Tetrameric Conformation
Bowman, A. J., Ward, R., Wiechens, N., Singh, V., Mkami, H. E., Norman, D., & Owen‐Hughes, T. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.01.025 · Cited by 82
Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State
Lee, T.-J., Pascuzzi, P. E., Settlage, S. B., Shultz, R. W., Tanurdžić, M., Rabinowicz, P. D., Menges, M., Zheng, P., Main, D., Murray, J. A. H., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000982 · Cited by 78
“Therefore, H3K56ac might be associated with nascent DNA behind active replication forks rather than the disassembly of chromatin ahead of replication forks [68].”
BackgroundChromatin Remodeling, DNA Damage Repair and Aging
Liu, B., Yip, R. K. H., & Zhou, Z. (2012) · Current Genomics · doi:10.2174/138920212803251373 · Cited by 81
Tanaka, A., Tanizawa, H., Sriswasdi, S., Iwasaki, O., Chatterjee, A. G., Speicher, D. W., Levin, H. L., Noguchi, E., & Noma, K.-I. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.09.011 · Cited by 78
“Modulation of Tf Clustering during the Cell Cycle and upon DNA Damage It has been shown that H3K56 acetylation is induced by Rtt109 during S phase in fission yeast and functions in DNA replication (Li et al., 2008; Ransom et al., 2010; Xhemalce et al., 2007).”
BackgroundEpigenetic regulation of genomic integrity
Deem, A. K., Li, X., & Tyler, J. K. (2012) · Chromosoma · doi:10.1007/s00412-011-0358-1 · Cited by 78
“PCNA (Li et al. 2008).”
Towards a mechanism for histone chaperones
Elsässer, S. J., & D’Arcy, S. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.07.007 · Cited by 73
“The multiple acetylation of H3-H4 in turn facilitates nuclear import and may enhance H3 affinity for CAF1 thereby promoting chromatin assembly [98, 100, 102, 103].”
BackgroundJack, A. P. M., Bussemer, S., Hahn, M., Pünzeler, S., Snyder, M., Wells, M. B., Csankovszki, G., Solovei, I. V., Schotta, G., & Hake, S. B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0051765 · Cited by 73
“It is most abundant during S phase [6,7] and has been shown to play a pivotal role in DNA damage response [6], chromatin integrity [8,9] and replication-coupled nucleosome assembly [10].”
BackgroundThe prenucleosome, a stable conformational isomer of the nucleosomePreprint
Fei, J., Torigoe, S. E., Brown, C. R., Khuong, M. T., Kassavetis, G. A., Boeger, H., & Kadonaga, J. T. (2015) · Genes & Development · doi:10.1101/gad.272633.115 · Cited by 73
“H3K56ac has been found to be involved in chromatin assembly during DNA replication and repair (for example, see Masumoto et al. 2005; Han et al. 2007; Chen et al. 2008; Li et al. 2008).”
BackgroundHistone modifications: crucial elements for damage response and chromatin restoration
Zhu, Q., & Wani, A. A. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22060 · Cited by 72
“Recent studies have uncovered a connection between H3K56 acetylation and chromatin assembly following DNA replication and DSB repair (Chen et al., 2008; Li et al., 2008).”
BackgroundYin, F., Lan, R., Zhang, X., Zhu, L., Chen, F., Xu, Z., Liu, Y., Ye, T., Sun, H., Lu, F., et al. (2013) · Molecular and Cellular Biology · doi:10.1128/mcb.00631-13 · Cited by 72
Regulation of histone gene transcription in yeast
Kurat, C. F., Recht, J., Radovani, E., Durbic, T., Andrews, B., & Fillingham, J. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1443-9 · Cited by 70
“During S phase, Rtt109–Asf1-catalyzed H3K56ac enhances RD chromatin assembly by increasing the interaction between H3–H4 dimers and Rtt106 and CAF-1 histone chaperones [80].”
BackgroundDefining the budding yeast chromatin‐associated interactome
Lambert, J., Fillingham, J., Siahbazi, M., Greenblatt, J., Baetz, K., & Figeys, D. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.104 · Cited by 73
“& 2010 EMBO and Macmillan Publishers Limited Molecular Systems Biology 2010 7 four baits revealed that HIR, Rtt106 and Asf1 associate with each other, whereas Rtt106 and CAF-1 compose another wellcharacterized complex (Huang et al, 2005, 2007; Li et al, 2008).”
Liu, W. H., Roemer, S. C., Zhou, Y., Shen, Z.-J., Dennehey, B. K., Balsbaugh, J. L., Liddle, J. C., Nemkov, T. G., Ahn, N. G., Hansen, K. C., et al. (2016) · eLife · doi:10.7554/elife.18023 · Cited by 71
“The cross-links in the vicinity of H3 K56 provide an explanation for the modulatory effect of H3 K56 acetylation on CAF-1 binding (Li et al., 2008; Winkler et al., 2012b).”
BackgroundWarren, C., & Shechter, D. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.06.005 · Cited by 70
“Pull-down studies using GST-tagged individual subunits show that Cac1 is the only subunit able to pull-down endogenous H3/H4 from HeLa cells [156].”
Ubiquitylation of FACT by the Cullin-E3 ligase Rtt101 connects FACT to DNA replicationPreprint
Han, J., Li, Q., McCullough, L. L., Kettelkamp, C., Formosa, T., & Zhang, Z. (2010) · Genes & Development · doi:10.1101/gad.1887310 · Cited by 72
“We and others have shown that acetylation of H3 Lys 56 by Rtt109 is important to promote efficient nucleosome assembly following DNA replication and DNA repair (Chen et al. 2008; Li et al. 2008).”
BackgroundMethodSelf-citationPeng, H., Nogueira, M. L., Vogel, J. L., & Kristie, T. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911128107 · Cited by 69
“The Asf1 proteins play critical roles in cellular DNA replication and repair processes by (i) modulating the flow of dissembled histones ahead of the advancing MCM replication fork (21), (ii) coordinating histone assembly on replicated and repaired DNA in conjunction with Chromatin Assembly Factor-1 (CAF-1) (29, 31),…”
Background
Metadata
- Authors
- Li, Q., Zhou, H., Wurtele, H., Davies, B., Horazdovsky, B., Verreault, A., & Zhang, Z.
- Affiliations
- Mayo Clinic (US)
- Institute for Research in Immunology and Cancer (CA)
- Corresponding author
- Verreault, Alain
- Zhang, Zhiguo
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2008-07
- Volume
- 134
- Issue
- 2
- Pages
- 244-255
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2597342
- OpenAlex
- W1965975821
- Cited by
- 447
- References
- 47
- Citations by year
- 2026: 14 · 2025: 11 · 2024: 12 · 2023: 20 · 2022: 15 · 2021: 23 · 2020: 14 · 2019: 16 · 2018: 20 · 2017: 22 · 2016: 35 · 2015: 22 · 2014: 34 · 2013: 32 · 2012: 35
- FWCI
- 16.61
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1842 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM072719, R01GM081838)
- 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 › Epigenetics and DNA Methylation
- Keywords
- histone H3 lysine 56 acetylation, CAF-1, histone chaperone, histone deposition, genome stability, histone acetylation, chromatin inheritance
- MeSH terms
- Acetylation, DNA Damage, DNA Replication, DNA, Fungal, Histones, Humans, Lysine, Mutation, Nucleosomes, Ribonucleases, Saccharomyces cerevisiae, S Phase, Protein Structure, Tertiary, Molecular Chaperones, Saccharomyces cerevisiae Proteins
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