Histone chaperones mediate the assembly and disassembly of nucleosomes and participate in essentially all DNA-dependent cellular processes. In Arabidopsis thaliana, loss-of-function of FAS1 or FAS2 subunits of the H3-H4 histone chaperone complex CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) has a dramatic effect on plant morphology, growth and overall fitness. CAF-1 dysfunction can lead to altered chromatin compaction, systematic loss of repetitive elements or increased DNA damage, clearly demonstrating its severity. How chromatin composition is maintained without functional CAF-1 remains elusive. Here we show that disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) suppresses the FAS1 loss-of-function phenotype. The quadruple mutant fas1 nap1;1 nap1;2 nap1;3 shows wild-type growth, decreased sensitivity to genotoxic stress and suppression of telomere and 45S rDNA loss. Chromatin of fas1 nap1;1 nap1;2 nap1;3 plants is less accessible to micrococcal nuclease and the nuclear H3.1 and H3.3 histone pools change compared to fas1. Consistently, association between NAP1 and H3 occurs in the cytoplasm and nucleus in vivo in protoplasts. Altogether we show that NAP1 proteins play an essential role in DNA repair in fas1, which is coupled to nucleosome assembly through modulation of H3 levels in the nucleus.

Centre for Molecular Medicine Central European Institute of Technology Masaryk University Kamenice 5 Brno CZ 62500 Czech Republic

Mendel Centre for Plant Genomics and Proteomics Central European Institute of Technology Masaryk University Kamenice 5 Brno CZ 62500 Czech Republic

Molecular Cytology and Cytometry Institute of Biophysics of the Czech Academy of Sciences v v i Královopolská 135 Brno CZ 61265 Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kotlářská 2 Brno CZ 61137 Czech Republic

Zobrazit více v PubMed

Almouzni, G. (2009) Chromatin assembly factors and the challenges of DNA replication and repair. FASEB J. 23. https://doi.org/10.1096/fasebj.23.1_supplement.421.1

Andrews, A.J., Downing, G., Brown, K., Park, Y.J. and Luger, K. (2008) A thermodynamic model for Nap1-histone interactions. J. Biol. Chem. 283, 32412-32418.

Andrews, A.J., Chen, X., Zevin, A., Stargell, L.A. and Luger, K. (2010) The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions. Mol. Cell, 37, 834-842.

Benoit, M., Simon, L., Desset, S., Duc, C., Cotterell, S., Poulet, A., Le Goff, S., Tatout, C. and Probst, A.V. (2019) Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. New Phytol. 221, 385-398.

Bouveret, R., Schonrock, N., Gruissem, W. and Hennig, L. (2006) Regulation of flowering time by Arabidopsis MSI1. Development, 133, 1693-1702.

Bowman, A., Ward, R., Wiechens, N., Singh, V., El-Mkami, H., Norman, D.G. and Owen-Hughes, T. (2011) The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation. Mol. Cell, 41, 398-408.

Chereji, R.V., Ocampo, J. and Clark, D.J. (2017) MNase-sensitive complexes in yeast: Nucleosomes and non-histone barriers. Mol Cell. 65, 565-577.

Citovsky, V., Lee, L.Y., Vyas, S., Glick, E., Chen, M.H., Vainstein, A., Gafni, Y., Gelvin, S.B. and Tzfira, T. (2006) Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. J. Mol. Biol. 362, 1120-1131.

D'Arcy, S., Martin, K.W., Panchenko, T., Chen, X., Bergeron, S., Stargell, L.A., Black, B.E. and Luger, K. (2013) Chaperone Nap1 shields histone surfaces used in a nucleosome and can put H2A-H2B in an unconventional tetrameric form. Mol. Cell, 51, 662-677.

Dellaporta, S.L., Wood, J. and Hicks, J.B. (1983) A plant DNA minipreparation: version II. Plant Mol. Biol. Report. 1, 19-21.

Dewari, P.S. and Bhargava, P. (2014) Genome-wide mapping of yeast histone chaperone anti-silencing function 1 reveals its role in condensin binding with chromatin. PLoS One, 9, e108652.

Dong, A., Liu, Z., Zhu, Y., Yu, F., Li, Z., Cao, K. and Shen, W.H. (2005) Interacting proteins and differences in nuclear transport reveal specific functions for the NAP1 family proteins in plants. Plant Physiol. 138, 1446-1456.

Dorn, A., Feller, L., Castri, D., Rohrig, S., Enderle, J., Herrmann, N.J., Block-Schmidt, A., Trapp, O., Kohler, L. and Puchta, H. (2019) An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability. PLoS Genet. 15, e1008174.

Dronamraju, R., Ramachandran, S., Jha, D.K., Adams, A.T., DiFiore, J.V., Parra, M.A., Dokholyan, N.V. and Strahl, B.D. (2017) Redundant functions for Nap1 and Chz1 in H2A.Z deposition. Sci. Rep. 7, 10791.

Duc, C., Benoit, M., Le Goff, S., Simon, L., Poulet, A., Cotterell, S., Tatout, C. and Probst, A.V. (2015) The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants. Plant J. 81, 707-722.

Duc, C., Benoit, M., Detourne, G. et al. (2017) Arabidopsis ATRX modulates H3.3 occupancy and fine-tunes gene expression. Plant Cell, 29, 1773-1793.

Dvorackova, M., Fojtova, M. and Fajkus, J. (2015) Chromatin dynamics of plant telomeres and ribosomal genes. Plant J. 83, 18-37.

Eckert-Boulet, N. and Lisby, M. (2010) Regulation of homologous recombination at telomeres in budding yeast. FEBS Lett. 584, 3696-3702.

Endo, M., Ishikawa, Y., Osakabe, K. et al. (2006) Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants. EMBO J. 25, 5579-5590.

Exner, V., Taranto, P., Schonrock, N., Gruissem, W. and Hennig, L. (2006) Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development. Development, 133, 4163-4172.

Fojtová, M., Fajkus, P., Polanská, P. and Fajkus, J. (2015) Terminal restriction fragments (TRF) method to analyze telomere lengths. Bio Protoc. 5, e1658.

Fulcher, N. and Sablowski, R. (2009) Hypersensitivity to DNA damage in plant stem cell niches. Proc. Natl Acad. Sci. USA, 106, 20984-20988.

Galbraith, D.W., Janda, J. and Lambert, G.M. (2011) Multiparametric analysis, sorting, and transcriptional profiling of plant protoplasts and nuclei according to cell type. Methods Mol. Biol. 699, 407-429.

Gao, J., Zhu, Y., Zhou, W., Molinier, J., Dong, A. and Shen, W.H. (2012) NAP1 family histone chaperones are required for somatic homologous recombination in Arabidopsis. Plant Cell, 24, 1437-1447.

Hammond, C.M., Stromme, C.B., Huang, H., Patel, D.J. and Groth, A. (2017) Histone chaperone networks shaping chromatin function. Nat. Rev. Mol. Cell Biol. 18, 141-158.

Haring, M., Offermann, S., Danker, T., Horst, I., Peterhansel, C. and Stam, M. (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods, 3, 11.

Hisanaga, T., Ferjani, A., Horiguchi, G. et al. (2013) The ATM-dependent DNA damage response acts as an upstream trigger for compensation in the fas1 mutation during arabidopsis leaf development. Plant Physiol. 162, 831-841.

Huang, T.H., Fowler, F., Chen, C.C., Shen, Z.J., Sleckman, B. and Tyler, J.K. (2018) The histone chaperones ASF1 and CAF-1 promote MMS22L-TONSL-mediated Rad51 loading onto ssDNA during homologous recombination in human cells. Mol. Cell, 69(5), 879-892.e5.

Chen, X., D'Arcy, S., Radebaugh, C.A., Krzizike, D.D., Giebler, H.A., Huang, L., Nyborg, J.K., Luger, K. and Stargell, L.A. (2016) Histone chaperone Nap1 is a major regulator of histone H2A-H2B dynamics at the inducible GAL locus. Mol. Cell. Biol. 36, 1287-1296.

Ishii, S., Koshiyama, A., Hamada, F.N., Nara, T.Y., Iwabata, K., Sakaguchi, K. and Namekawa, S.H. (2008) Interaction between Lim15/Dmc1 and the homologue of the large subunit of CAF-1: a molecular link between recombination and chromatin assembly during meiosis. FEBS J. 275, 2032-2041.

Ivics, Z. and Izsvak, Z. (2010) Repetitive elements and genome instability. Semin. Cancer Biol. 20, 197-199.

Jacob, Y., Bergamin, E., Donoghue, M.T. et al. (2014) Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science, 343, 1249-1253.

Jin, C., Zang, C., Wei, G., Cui, K., Peng, W., Zhao, K. and Felsenfeld, G. (2009) H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet. 41, 941-945.

Kaufman, P.D., Kobayashi, R., Kessler, N. and Stillman, B. (1995) The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell, 81, 1105-1114.

Kaya, H., Shibahara, K.I., Taoka, K.I., Iwabuchi, M., Stillman, B. and Araki, T. (2001) FASCIATA genes for chromatin assembly factor-1 in arabidopsis maintain the cellular organization of apical meristems. Cell, 104, 131-142.

Kirik, A., Pecinka, A., Wendeler, E. and Reiss, B. (2006) The chromatin assembly factor subunit FASCIATA1 is involved in homologous recombination in plants. Plant Cell, 18, 2431-2442.

Kobayashi, T., Horiuchi, T., Tongaonkar, P., Vu, L. and Nomura, M. (2004) SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell, 117, 441-453.

Lankenau, S., Barnickel, T., Marhold, J., Lyko, F., Mechler, B.M. and Lankenau, D.H. (2003) Knock-out targeting of the Drosophila Nap1 gene and examination of DNA repair tracts in the recombination products. Genetics, 163, 611-623.

Ledvinova, D., Mikulasek, K., Kucharikova, H., Brabencova, S., Fojtova, M., Zdrahal, Z. and Lochmanova, G. (2018) Filter-aided sample preparation procedure for mass spectrometric analysis of plant histones. Front. Plant Sci. 9, 1373.

Levine, A.J., Ting, D.T. and Greenbaum, B.D. (2016) P53 and the defenses against genome instability caused by transposons and repetitive elements. BioEssays, 38, 508-513.

Liu, Z., Zhu, Y., Gao, J., Yu, F., Dong, A. and Shen, W.H. (2009) Molecular and reverse genetic characterization of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) genes unravels their function in transcription and nucleotide excision repair in Arabidopsis thaliana. Plant J. 59, 27-38.

Lundin, C., North, M., Erixon, K., Walters, K., Jenssen, D., Goldman, A.S. and Helleday, T. (2005) Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucleic Acids Res. 33, 3799-3811.

Ma, J., Liu, Y., Zhou, W., Zhu, Y., Dong, A. and Shen, W.H. (2018) Histone chaperones play crucial roles in maintenance of stem cell niche during plant root development. Plant J. 95, 86-100.

Manova, V. and Gruszka, D. (2015) DNA damage and repair in plants - from models to crops. Front. Plant Sci. 6, 885.

McBryant, S.J., Park, Y.J., Abernathy, S.M., Laybourn, P.J., Nyborg, J.K. and Luger, K. (2003) Preferential binding of the histone (H3-H4)2 tetramer by NAP1 is mediated by the amino-terminal histone tails. J. Biol. Chem. 278, 44574-44583.

Mello, J.A., Sillje, H.H.W., Roche, D.M.J., Kirschner, D.B., Nigg, E.A. and Almouzni, G. (2002) Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway. EMBO Rep. 3, 329-334.

Miyaji-Yamaguchi, M., Kato, K., Nakano, R., Akashi, T., Kikuchi, A. and Nagata, K. (2003) Involvement of nucleocytoplasmic shuttling of yeast Nap1 in mitotic progression. Mol. Cell. Biol. 23, 6672-6684.

Moshkin, Y.M., Doyen, C.M., Kan, T.W., Chalkley, G.E., Sap, K., Bezstarosti, K., Demmers, J.A., Ozgur, Z., van Ijcken, W.F. and Verrijzer, C.P. (2013) Histone chaperone NAP1 mediates sister chromatid resolution by counteracting protein phosphatase 2A. PLoS Genet. 9, e1003719.

Mozgova, I., Mokros, P. and Fajkus, J. (2010) Dysfunction of chromatin assembly factor 1 induces shortening of telomeres and loss of 45S rDNA in Arabidopsis thaliana. Plant Cell, 22, 2768-2780.

Mozgova, I., Wildhaber, T., Trejo-Arellano, M.S., Fajkus, J., Roszak, P., Kohler, C. and Hennig, L. (2018) Transgenerational phenotype aggravation in CAF-1 mutants reveals parent-of-origin specific epigenetic inheritance. New Phytol. 220(3), 908-921.

Mozgova, I., Wildhaber, T., Liu, Q., Abou-Mansour, E., L'Haridon, F., Metraux, J.P., Gruissem, W., Hofius, D. and Hennig, L. (2015) Chromatin assembly factor CAF-1 represses priming of plant defence response genes. Nat. Plants, 1, 15127.

Muchova, V., Amiard, S., Mozgova, I., Dvorackova, M., Gallego, M.E., White, C. and Fajkus, J. (2015) Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants. Plant J. 81, 198-209.

Munoz-Viana, R., Wildhaber, T., Trejo-Arellano, M.S., Mozgova, I. and Hennig, L. (2017) Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes. Plant J. 92, 363-374.

Nakagawa, T., Bulger, M., Muramatsu, M. and Ito, T. (2001) Multistep chromatin assembly on supercoiled plasmid DNA by nucleosome assembly protein-1 and ATP-utilizing chromatin assembly and remodeling factor. J. Biol. Chem. 276, 27384-27391.

Otero, S., Desvoyes, B., Peiro, R. and Gutierrez, C. (2016) Histone H3 dynamics reveal domains with distinct proliferation potential in the arabidopsis root. Plant Cell, 28, 1361-1371.

Ozer, O. and Hickson, I.D. (2018) Pathways for maintenance of telomeres and common fragile sites during DNA replication stress. Open Biol. 8, 180018.

Pavlistova, V., Dvorackova, M., Jez, M., Mozgova, I., Mokros, P. and Fajkus, J. (2016) Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes. Plant J. 88, 411-424.

Pecinka, A. and Liu, C.H. (2014) Drugs for plant chromosome and chromatin research. Cytogenet. Genome Res. 143, 51-59.

Peterson, R., Slovin, J.P. and Chen, C. (2010) A simplified method for differential staining of aborted and non-aborted pollen grains. Int. J. Plant Biol. 1, 13.

Pfab, A., Breindl, M. and Grasser, K.D. (2018) The Arabidopsis histone chaperone FACT is required for stress-induced expression of anthocyanin biosynthetic genes. Plant Mol. Biol. 96, 367-374.

Pizzolato, J.F. and Saltz, L.B. (2003) The camptothecins. Lancet, 361, 2235-2242.

Pontvianne, F., Blevins, T., Chandrasekhara, C. et al. (2013) Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes Dev. 27, 1545-1550.

Prasad, R., D'Arcy, S., Hada, A., Luger, K. and Bartholomew, B. (2016) Coordinated action of Nap1 and RSC in disassembly of tandem nucleosomes. Mol. Cell Biol. 36, 2262-2271.

Ramirez-Parra, E. and Gutierrez, C. (2007) E2F regulates FASCIATA1, a chromatin assembly gene whose loss switches on the endocycle and activates gene expression by changing the epigenetic status. Plant Physiol. 144, 105-120.

Rogner, U.C., Spyropoulos, D.D., Le Novere, N., Changeux, J.P. and Avner, P. (2000) Control of neurulation by the nucleosome assembly protein-1-like 2. Nat. Genet. 25, 431-435.

Rohrig, S., Schropfer, S., Knoll, A. and Puchta, H. (2016) The RTR complex partner RMI2 and the DNA helicase RTEL1 are both independently involved in preserving the stability of 45S rDNA repeats in Arabidopsis thaliana. PLoS Genet. 12, e1006394.

Roudier, F., Ahmed, I., Berard, C. et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928-1938.

Sequeira-Mendes, J., Araguez, I., Peiro, R., Mendez-Giraldez, R., Zhang, X., Jacobsen, S.E., Bastolla, U. and Gutierrez, C. (2014) The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. Plant Cell, 26, 2351-2366.

Sfeir, A., Kosiyatrakul, S.T., Hockemeyer, D., MacRae, S.L., Karlseder, J., Schildkraut, C.L. and de Lange, T. (2009) Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Cell, 138, 90-103.

Shimada, M., Chen, W.Y., Nakadai, T., Onikubo, T., Guermah, M., Rhodes, D. and Roeder, R.G. (2019) Gene-specific H1 eviction through a transcriptional activator p300 NAP1 H1 pathway. Mol. Cell, 74(2), 268-283.e5.

Schrumpfova, P.P., Fojtova, M., Mokros, P., Grasser, K.D. and Fajkus, J. (2011) Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana. Curr. Protein Pept. Sci. 12, 105-111.

Slamenova, D., Dusinska, M., Bastlova, T. and Gabelova, A. (1990) Differences between survival, mutagenicity and DNA replication in MMS- and MNU-treated V79 hamster cells. Mutat. Res. 228, 97-103.

Takeuchi, Y., Horiuchi, T. and Kobayashi, T. (2003) Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17, 1497-1506.

Tyler, J.K., Collins, K.A., Prasad-Sinha, J., Amiott, E., Bulger, M., Harte, P.J., Kobayashi, R. and Kadonaga, J.T. (2001) Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol. Cell Biol. 21, 6574-6584.

Vannier, J.B., Depeiges, A., White, C. and Gallego, M.E. (2009) ERCC1/XPF protects short telomeres from homologous recombination in Arabidopsis thaliana. PLoS Genet. 5, e1000380.

Varas, J., Santos, J.L. and Pradillo, M. (2017) The absence of the arabidopsis chaperone complex CAF-1 produces mitotic chromosome abnormalities and changes in the expression profiles of genes involved in DNA repair. Front. Plant Sci. 8, 525.

Varas, J., Sanchez-Moran, E., Copenhaver, G.P., Santos, J.L. and Pradillo, M. (2015) Analysis of the relationships between DNA double-strand breaks, synaptonemal complex and crossovers using the Atfas1-4 mutant. PLoS Genet. 11, e1005301.

Wollmann, H., Stroud, H., Yelagandula, R. et al. (2017) The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol. 18, 94.

Xi, Y., Yao, J., Chen, R., Li, W. and He, X. (2011) Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. Genome Res. 21, 718-724.

Yelagandula, R., Stroud, H., Holec, S. et al. (2014) The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell, 158, 98-109.

Zhang, H., Xiong, Y. and Chen, J. (2020) DNA-protein cross-link repair: what do we know now? Cell Biosci. 10, 3.

Zhang, Q., Giebler, H.A., Isaacson, M.K. and Nyborg, J.K. (2015) Eviction of linker histone H1 by NAP-family histone chaperones enhances activated transcription. Epigenetics Chromatin, 8, 30.

Zhou, W., Gao, J., Ma, J., Cao, L., Zhang, C., Zhu, Y., Dong, A. and Shen, W.H. (2016) Distinct roles of the histone chaperones NAP1 and NRP and the chromatin-remodeling factor INO80 in somatic homologous recombination in Arabidopsis thaliana. Plant J. 88, 397-410.

Zhu, Y., Dong, A., Meyer, D., Pichon, O., Renou, J.P., Cao, K. and Shen, W.H. (2006) Arabidopsis NRP1 and NRP2 encode histone chaperones and are required for maintaining postembryonic root growth. Plant Cell, 18, 2879-2892.

Zhu, Y., Weng, M., Yang, Y., Zhang, C., Li, Z., Shen, W.H. and Dong, A. (2011) Arabidopsis homologues of the histone chaperone ASF1 are crucial for chromatin replication and cell proliferation in plant development. Plant J. 66, 443-455.

Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications

In-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants

Telomerase Interaction Partners-Insight from Plants

G2/M-checkpoint activation in fasciata1 rescues an aberrant S-phase checkpoint but causes genome instability

The rDNA Loci-Intersections of Replication, Transcription, and Repair Pathways