The histone variant Sl_H2A.Z regulates carotenoid biosynthesis and gene expression during tomato fruit ripening

Abstract

The conserved histone variant H2A.Z is essential for transcriptional regulation; defense responses; and various biological processes in plants, such as growth, development, and flowering. However, little is known about how H2A.Z affects the developmental process and ripening of tomato fruits. Here, we utilized the CRISPR/Cas9 gene-editing system to generate a sl_hta9 sl_hta11 double-mutant, designated sl_h2a.z, and found that these two mutations led to a significant reduction in the fresh weight of tomato fruits. Subsequent messenger RNA (mRNA)-seq results showed that dysfunction of Sl_H2A.Z has profound effects on the reprogramming of genome-wide gene expression at different developmental stages of tomato fruits, indicating a ripening-dependent correlation between Sl_H2A.Z and gene expression regulation in tomato fruits. In addition, the expression of three genes, SlPSY1, SlPDS, and SlVDE, encoding the key enzymes in the biosynthesis pathway of carotenoids, was significantly upregulated in the later ripening stages, which was consistent with the increased contents of carotenoids in sl_h2a.z double-mutant fruits. Overall, our study reveals a role of Sl_H2A.Z in the regulation of carotenoids and provides a resource for the study of Sl_H2A.Z-dependent gene expression regulation. Hence, our results provide a link between epigenetic regulation via histone variants and fruit development, suggesting a conceptual framework to understand how histone variants regulate tomato fruit quality.

References

[1] Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707-719 (2007).

[2] Lai, W. K. M. & Pugh, B. F. Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat. Rev. Mol. Cell Biol. 18, 548-562 (2017).

[3] Berriri, S., Gangappa, S. N. & Kumar, S. V. SWR1 chromatin-remodeling complex subunits and H2A.Z have non-overlapping functions in immunity and gene regulation in Arabidopsis. Mol. Plant 9, 1051-1065 (2016).

[4] Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260 (1997).

[5] Yelagandula, R. et al. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 158, 98-109 (2014).

[6] Nie, W. F. et al. Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis. Proc. Natl Acad. Sci. USA 116, 16641-16650 (2019).

[7] Lei, B. & Berger, F. H2A variants in Arabidopsis: versatile regulators of genome activity. Plant Commun. 1, 100015 (2020).

[8] Kumar, S. V. H2A.Z at the core of transcriptional regulation in plants. Mol. Plant 11, 1112-1114 (2018).

[9] Greenberg, R. S., Long, H. K., Swigut, T. & Wysocka, J. Single amino acid change underlies distinct roles of H2A.Z subtypes in human syndrome. Cell 178, 1421-1436.e1424 (2019).

[10] Ranjan, A. et al. Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell 154, 1232-1245 (2013).

[11] Papamichos-Chronakis, M., Watanabe, S., Rando, O. J. & Peterson, C. L. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell 144, 200-213 (2011).

[12] Zhang, K. et al. Differential deposition of H2A.Z in combination with histone modifications within related genes in Oryza sativa callus and seedling. Plant J. 89, 264-277 (2017).

[13] Li, Z. et al. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 151, 1608-1616 (2012).

[14] Dai, X. et al. H2A.Z represses gene expression by modulating promoter nucleosome structure and enhancer histone modifications in Arabidopsis. Mol. Plant 10, 1274-1292 (2017).

[15] Sura, W. et al. Dual role of the histone variant H2A.Z in transcriptional reg-ulation of stress-response genes. Plant Cell 29, 791-807 (2017).

[16] Zahraeifard, S. et al. Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes. J. Exp. Bot. 69, 4907-4919 (2018).

[17] Thakar, A. et al. H2A.Z and H3.3 histone variants affect nucleosome struc-ture: biochemical and biophysical studies. Biochem.-Us 48, 10852-10857 (2009).

[18] Kumar, S. V. & Wigge, P. A. H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140, 136-147 (2010).

[19] Talbert, P. B. & Henikoff, S. Environmental responses mediated by histone variants. Trends Cell Biol. 24, 642-650 (2014).

[20] Yi, H. et al. Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family mem-bers. Plant Cell 18, 1575-1589 (2006).

[21] Coleman-Derr, D. & Zilberman, D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 8, e1002988 (2012).

[22] Seymour, G. B., Ostergaard, L., Chapman, N. H., Knapp, S. & Martin, C. Fruit development and ripening. Annu. Rev. Plant Biol. 64, 219-241 (2013).

[23] Klee, H. J. & Giovannoni, J. J. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45, 41-59 (2011).

[24] Teyssier, E. et al. Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta 228, 391-399 (2008).

[25] Hadfield, K., Dandekar, A. & Romani, R. Demethylation o fripening specific genes in tomato fruit. Plant Sci. 92, 13-18 (1993).

[26] Lang, Z. et al. Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc. Natl Acad. Sci. USA 114, E4511-E4519 (2017).

[27] Liu, R. et al. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl Acad. Sci. USA 112, 10804-10809 (2015).

[28] Tang, D., Gallusci, P. & Lang, Z. Fruit development and epigenetic modifica-tions. New Phytol. https://doi.org/10.1111/nph.16724 (2020).

[29] Guo, J. E. et al. Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato. Plant Sci. 265, 29-38 (2017).

[30] Deal, R. B., Topp, C. N., McKinney, E. C. & Meagher, R. B. Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 19, 74-83 (2007).

[31] Talbert, P. B. et al. A unified phylogeny-based nomenclature for histone var-iants. Epigenetics Chromatin 5, 7 (2012).

[32] Kawashima, T. et al. Diversification of histone H2A variants during plant evo-lution. Trends Plant Sci. 20, 419-425 (2015).

[33] Mao, Y. et al. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol. Plant 6, 2008-2011 (2013).

[34] March-Diaz, R. & Reyes, J. C. The beauty of being a variant: H2A.Z and the SWR1 complex in plants. Mol. Plant 2, 565-577 (2009).

[35] Huang, H. et al. Global increase in DNA methylation during orange fruit development and ripening. Proc. Natl Acad. Sci. USA 116, 1430-1436 (2019).

[36] Milani, A., Basirnejad, M., Shahbazi, S. & Bolhassani, A. Carotenoids: biochem-istry, pharmacology and treatment. Br. J. Pharm. 174, 1290-1324 (2017).

[37] Jomova, K. & Valko, M. Health protective effects of carotenoids and their interactions with other biological antioxidants. Eur. J. Med. Chem. 70, 102-110 (2013).

[38] Rutz, J. K., Borges, C. D., Zambiazi, R. C., da Rosa, C. G. & da Silva, M. M. Elaboration of microparticles of carotenoids from natural and synthetic sources for applications in food. Food Chem. 202, 324-333 (2016).

[39] Giaimo, B. D., Ferrante, F., Herchenrother, A., Hake, S. B. & Borggrefe, T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 12, 37 (2019).

[40] Gomez-Zambrano, A. et al. Arabidopsis SWC4 binds DNA and recruits the SWR1 complex to modulate histone H2A.Z deposition at key regulatory genes. Mol. Plant 11, 815-832 (2018).

[41] Boden, S. A., Kavanova, M., Finnegan, E. J. & Wigge, P. A. Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes. Genome Biol. 14, R65 (2013).

[42] Cortijo, S. et al. Transcriptional regulation of the ambient temperature response by H2A.Z nucleosomes and HSF1 transcription factors in Arabi-dopsis. Mol. Plant 10, 1258-1273 (2017).

[43] Zhong, S. et al. Single-base resolution methylomes of tomato fruit develop-ment reveal epigenome modifications associated with ripening. Nat. Bio-technol. 31, 154-159 (2013).

[44] Zuo, J. et al. Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit. Plant J. https://doi.org/10.1111/tpj.14778 (2020).

[45] Ioannidi, E. et al. Expression profiling of ascorbic acid-related genes during tomato fruit development and ripening and in response to stress conditions. J. Exp. Bot. 60, 663-678 (2009).

[46] Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170-S180 (2004).

[47] Raisner, R. M. et al. Histone variant H2A.Z marks the 5’ ends of both active and inactive genes in euchromatin. Cell 123, 233-248 (2005).

[48] Hall, H. et al. Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence. BMC Genomics 18, 894 (2017).

[49] Del Olmo, I., Poza-Viejo, L., Pineiro, M., Jarillo, J. A. & Crevillen, P. High ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics. Plant J. 100, 343-356 (2019).

[50] Fitter, A. H. & Fitter, R. S. R. Rapid changes in flowering time in British plants. Science 296, 1689-1691 (2002).

[51] Franklin, K. A. Plant chromatin feels the heat. Cell 140, 26-28 (2010).

[52] Deal, R. B. & Henikoff, S. Gene regulation: a chromatin thermostat. Nature 463, 887-888 (2010).

[53] Alexander, L. & Grierson, D. Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. J. Exp. Bot. 53, 2039-2055 (2002).

[54] Eggersdorfer, M. & Wyss, A. Carotenoids in human nutrition and health. Arch. Biochem. Biophys. 652, 18-26 (2018).

[55] Fiedor, J. & Burda, K. Potential role of carotenoids as antioxidants in human health and disease. Nutrients 6, 466-488 (2014).

[56] Rao, A. V. & Rao, L. G. Carotenoids and human health. Pharm. Res. 55, 207-216 (2007).

[57] Zilberman, D., Coleman-Derr, D., Ballinger, T. & Henikoff, S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456, 125-129 (2008).

[58] Grimanelli, D. & Ingouff, M. DNA methylation readers in plants. J. Mol. Biol. https://doi.org/10.1016/j.jmb.2019.12.043 (2020).

[59] Jiang, G. et al. Redox regulation of the NOR transcription factor is involved in the regulation of fruit ripening in tomato. Plant Physiol. https://doi.org/10.1104/pp.20.00070 (2020).

[60] Li, Y. et al. MicroTom metabolic network: rewiring tomato metabolic reg-ulatory network throughout the growth cycle. Mol. Plant https://doi.org/10.1016/j.molp.2020.06.005. (2020).

[61] Saravana Kumar, R., M. et al . Redox components: key regulators of epigenetic modifications in plants. Int. J. Mol. Sci. 21, https://doi.org/10.3390/ijms21041419 (2020).

[62] Reczek, C. R. & Chandel, N. S. ROS-dependent signal transduction. Curr. Opin. Cell Biol. 33, 8-13 (2015).

[63] Gill, S. S. & Tuteja, N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol. Biochem. 48, 909-930 (2010).

[64] Hancock, J. T., Desikan, R. & Neill, S. J. Role of reactive oxygen species in cell signalling pathways. Biochem. Soc. Trans. 29, 345-350 (2001).

[65] Schieber, M. & Chandel, N. S. ROS function in redox signaling and oxidative stress. Curr. Biol. 24, R453-R462 (2014).

[66] Ray, P. D., Huang, B. W. & Tsuji, Y. Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling. Cell Signal. 24, 981-990 (2012).

[67] Meng, X. et al. Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation. Biochim. Biophys. Acta Proteins Proteom. 1866, 451-463 (2018).

[68] Shi, L., Wang, J., Hong, F., Spector, D. L. & Fang, Y. Four amino acids guide the assembly or disassembly of Arabidopsis histone H3.3-containing nucleosomes. Proc. Natl Acad. Sci. USA 108, 10574-10578 (2011).

[69] Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).

[70] Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290-295 (2015).

[71] Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).

[72] Garber, M., Grabherr, M. G., Guttman, M. & Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8, 469-477 (2011).

[73] Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).