Histone modification changes under abiotic stress conditions
Post-translational modification of histone N-tails affects eukaryotic gene activity (Wu & Grunstein 2000; Millar & Grunstein 2006). In Arabidopsis, 28 histone modification sites have been identified by mass spectrometry and chromatin immunoprecipitation (ChIP) analyses (Zhang et al. 2007b; Kim et al. 2008). Recently, several reports on the changes in histone modification under abiotic stresses in plants have been published.
ChIP assay showed that histone modifications on the H3 N-tail are altered with gene activation on the coding regions of four Arabidopsis drought stress-responsive genes such as responsive to dehydration (RD)29A, RD29B and RD20, and an AP2 domain-containing transcription factor (At2g20880) in response to drought stress (Fig. 1; Kim et al. 2008). Enrichments of trimethylation of histone H3 Lys4 (H3K4me3) and acetylation of histone H3 Lys9 (H3K9ac), often used as a positive marker of histone modifications associated with gene activity, correlate with gene activation in response to drought stress in all four drought-inducible genes. Enrichment of acetylation of histone H3 Lys23 (H3K23ac) and acetylation of histone H3 Lys27 (H3K27ac) occurs in response to drought stress on the coding regions of RD29B, RD20 and At2g20880, but not on the coding region of RD29A, indicating that enrichment of H3K23ac and H3K27ac occurs in response to drought stress in a gene-specific manner. Interestingly, establishment of H3K4me3 enrichment occurs after full activation of RD29A and At2g20880 transcription in response to drought stress.
Figure 1. A possible chromatin regulation mechanism involving changes in histone modification and nucleosome occupancy in response to drought stress. Chromatin regulation-related components are shown in red. HAT, histone acetyltransferase; HDAC, histone deacetylase; HMG, high-mobility group (HMG) proteins; HMT, histone methyltransferase; H1–3, linker histone H1–3; RNAPII, RNA polymerase II; TF, transcription factor. See text for details.
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Kwon et al. (2009) showed that trimethylation of histone H3 Lys27 (H3K27me3), a negative histone modification marker for transcription, is decreased in two Arabidopsis cold-responsive genes, cold-regulated (COR)15A and ATGOLS3 (Taji et al. 2002) encoding galactinol synthase (GOLS), during exposure to cold temperature by ChIP assay. The decrease of H3K27me3 is maintained for up to 3 d after a return to normal growth temperature, while the mRNA accumulation of the COR15A and ATGOLS3 was repressed at 1 d after the removal of the cold stress. These results suggest that enrichment of H3K27me3 can be inherited to some degree through cell divisions. However, the previous cold-induced decrease of H3K27me3 level of the two genes did not enhance the transcriptional induction after re-exposure to cold stress.
Sokol et al. (2007) applied Western blot analysis to study nucleosomal response in cultured cells of Arabidopsis T87 and tobacco BY-2 cell lines, and showed that phosphorylation of histone H3 Ser10, phosphoacetylation of histone H3 at Ser10 and Lys14 and acetylation of histone H4 were increased by high-salinity, cold and abscisic acid (ABA) treatments. The observed nucleosomal response was consistent with the up-regulation of the stress-inducible genes.
In rice, modification levels of acetylation of histone H3, dimethylation of histone H3 Lys4 (H3K4me2) and trimethylation of histone H3 Lys4 (H3K4me3) were altered on submergence-inducible genes, alcohol dehydrogenase 1 (ADH1) and pyruvate decarboxylase 1 (PDC1) during the process from submergence to re-aeration (Tsuji et al. 2006). The submergence treatments resulted in the decrease of H3K4me2 levels and increase of H3K4me3 levels on the 5′- and 3′-coding regions of ADH1 and PDC1 genes. Histone H3 acetylation was gradually increased on the ADH1 and PDC1 genes with submergence treatment. These histone modification levels recovered to the initial levels after re-aeration treatment.
Histone modification enzymes
Changes in chromatin structures are related with modification of the N-terminal tails of the histones. Histone modification enzymes, such as histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT) and histone demethylase (HDM), function in the modification of the N-terminal tails of the histones, and are an essential factor for chromatin remodeling (Fig. 1).
Several HATs are responsible for transcriptional activation through the acetylation of lysine residues on the histone N-tails (Fukuda et al. 2006; Earley et al. 2007). In Arabidopsis, there are 12 HAT proteins including three members of general control non-derepressible (GCN5)-related N-terminal acetyltransferase (GNAT) family, two members of MOZ, YbF2, Sas2, Tip60-like (MYST) family, five members of CREB-binding protein (CBP) homolog and two members of TAF-II-250 homolog (Pandey et al. 2002). Their information is also available at the Chromatin Database (http://www.chromdb.org/).
Table 1. Major findings on histone modification enzymes and chromatin-associated proteins involved in the response to drought, cold and high-salinity stress
|Organism||Functional category||Gene||Phenotype of mutants or transgenic plants/functional characteristic||Reference|
|Arabidopsis||HAT||AtGCN5||Involved in transcriptional responses to cold stress||Stockinger et al. (2001) Vlachonasios et al. (2003)|
| ||Transcriptional adaptor protein||Ada2b||Freezing tolerance phenotype in ada2b mutants||Vlachonasios et al. (2003)|
| ||Subunit of Elongator HAT complex||ELP2 ELP6 ELP42/ELO1 ELP1/ABO1/ELO2||Phenotypes of oxidative stress tolerance, ABA hypersensitivity and increased accumulation of anthocyanin in the mutants of four subunits||Zhou et al. (2009)|
| ||HDAC||AtHD2C||Salinity stress tolerance phenotype in transgenic plants over-expressing AtHD2C||Sridha & Wu (2006)|
| ||Homolog of human TBC||HOS15||Freezing stress-hypersensitive phenotype in hos15 mutants||Zhu et al. (2008)|
| ||Subunit of Polycomb group protein complexes||MSI1||Drought stress tolerance phenotype in co-suppression transgenic plants of MSI1||Alexandre et al. (2009)|
| ||Linker histone H1||HIS1–3||Up-regulation of drought stress and ABA; a target gene regulated by AREB1||Ascenzi & Gantt (1997) Fujita et al. (2005)|
| ||HMG protein||HMGB1||Phenotype of decreased seed germination rate in transgenic plants over-expressing HMGB1||Lildballe et al. (2008)|
| || ||HMGB2||Phenotypes of retarded germination and subsequent growth in transgenic plants over-expressing HMGB2||Kwak et al. (2007)|
| ||ATP-dependent chromatin remodeling factor||AtCHR12||Phenotype of growth arrest of primary buds and stems under the drought and heat stress in transgenic plants overexpressing AtCHR12||Mlynárová, Nap & Bisseling (2007)|
| || || ||Phenotype of less growth arrest under the drought and heat stress in atchr12 mutants|| |
| || ||SWI3B||Phenotype of reduced sensitivity to ABA-mediated inhibition of seed germination and growth in swi3b mutants||Saez et al. (2008)|
|Tomato||Linker histone H1||HIS1-S||Phenotypes of faster decrease in relative water content of leaves, higher stomatal conductance and higher transpiration rate in antisense transgenic plants of HIS1-S||Scippa et al. (2004)|
The yeast two-hybrid assay showed that AtGCN5 interacts with a protein phosphatase 2C protein (AtPP2C-6-6) (Servet et al. 2008). The AtGCN5 protein is dephosphorylated by AtPP2C-6-6 in vitro. Expression of several stress-inducible genes, responsive to ABA (RAB)18, RD29A, RD29B and COR15A, were reduced under the high-salinity stress in atpp2c-6-6 mutants, while in the atgcn5 mutants, the expression of the stress-inducible genes was not affected by high-salinity stress, but the expression of RAB18 and RD29B was increased in unstressed condition. Western blot analysis showed that acetylation levels of histone H3K14 and H3K27 were not changed greatly in atpp2c-6-6 mutants and that these histone acetylation levels were reduced in atgcn5 mutants. Although these results indicate that AtPP2C-6-6 is required for the induction of several stress-inducible genes, it is not clear whether the function of AtPP2C-6-6 in stress responses is achieved through its interaction with AtGCN5.
The mutants of the Arabidopsis homologs of the four subunits of yeast Elongator HAT complex, ELP2, ELP6, ELP42/ELO1 and ELP1/ABA-overly sensitive 1 (ABO1)/ELO2 (Chen et al. 2006) showed the phenotypes of oxidative stress tolerance, ABA hypersensitivity and increased accumulation of anthocyanin (Zhou et al. 2009; Table 1). Among them, the mutations in the ELP1/ABO1/ELO2 and ELP2 genes caused stomatal closing and ABA supersensitivity. The four mutants of the Elongator subunits had increased transcript levels of a catalase (CAT3) gene under normal conditions and of ZAT10 (Mittler et al. 2006) gene, a C2H2-zinc finger-type transcription factor whose gain- and loss-of-function mutations enhance the tolerance to salinity, heat and osmotic stress. These results suggest that Elongator plays a role in regulating ABA responses and oxidative stress tolerance.
HDACs are generally responsible for repression of gene activity through the deacetylation of lysine residue on the histone N-tails. In Arabidopsis, there are 18 HDACs, including 12 members of RPD3/HDA1 superfamily, four members of plant-specific HD2 family and two members of SIR2 family.
Gene expression of the HD2C, a plant-specific HD2-type HDAC in Arabidopsis, was repressed by ABA treatment (Sridha & Wu 2006). 35S:AtHD2C-GFP seedlings were insensitive to ABA. In wild-type plants, seed germination and root elongation were inhibited at 0.1 µM ABA. On the other hand, they were not inhibited in 35S:AtHD2C-GFP transgenic plants under the same conditions. In addition, at 100 mm NaCl, germination and root elongation of 35S:AtHD2C-GFP plants were not inhibited compared with wild-type plants (Table 1). Expression of several ABA-responsive genes, such as RD29B and RAB18, was up-regulated in 35S:AtHD2C-GFP plants, indicating that AtHD2C can modulate ABA and stress responses.
The Arabidopsis high expression of osmotically responsive genes (hos) 15 mutant was hypersensitive to freezing stress (Zhu et al. 2008; Table 1). HOS15 encodes a protein similar to human transducin-β-like protein (TBC), a component of a repressor protein complex involved in histone deacetylation. The acetylation level of histone H4 was higher in the hos15 mutants than in wild-type plants, suggesting that HOS15 is involved in deacetylation of histone H4.
In rice, there are 18 HDACs including 14 members of RPD3/HDA1 superfamily, two members of HD2 family and two members of SIR2 family. Semi-quantitative RT-PCR analysis revealed that the expression of several rice HDAC genes respond differently to abiotic stresses and to hormones such as ABA (Fu, Wu & Duan 2007). ABA repressed the expression of HDT701 and SRT701 genes, members of HD2 family and SRT702 gene, a member of SIR2 family. Abiotic stresses, such as mannitol and cold stress, repressed the expression of SRT701 gene. In barley, semi-quantitative RT-PCR analysis revealed that the expression of HvHDAC2-2 gene, a member of HD2 family, was repressed at 6 h after ABA treatment (Demetriou et al. 2009). Recent Arabidopsis tiling array analysis also showed that the expression of several chromatin regulation-related genes including histone modification enzymes is influenced by drought, high-salinity stress and ABA (Matsui et al. 2008).
Recently, the transgenic Arabidopsis co-suppression lines (msi1-cs) of MSI1 gene, encoding a subunit of Polycomb group protein complexes and chromatin assembly factor 1, showed increased drought stress tolerance phenotype (Alexandre et al. 2009; Table 1). In the msi1-cs lines, the expression of many ABA-responsive genes were up-regulated. The ChIP assay demonstrated that the drought-inducible RD20 gene is a direct target of MSI1.
Changes in nucleosome occupancy under abiotic stress conditions
Generally, nucleosome occupancy is negatively correlated with transcriptional activation. When the transcription is activated in a genomic region, nucleosome density is decreased and the chromatin structure is relaxed (Clark & Felsenfeld 1991; Eberharter & Becker 2002).
The ChIP assay using anti-histone H3 C-terminal antibody indicated that two types of regulation of nucleosome occupancy function in the drought stress response (Fig. 1; Kim et al. 2008). The first type is that nucleosome density on the promoter regions is low compared with that of coding regions, and there is no notable nucleosome loss on the coding regions under drought stress. This type is observed in RD29A and RD29B genes (Fig. 1). Note that the nucleosome density of RD29A and RD29B promoter regions containing key drought stress-responsive cis-elements, dehydration-responsive element (DRE)/C-repeat (CRT) (Yamaguchi-Shinozaki & Shinozaki 1994) or ABA-responsive element (ABRE) (Yamaguchi-Shinozaki & Shinozaki 1994) motifs is low. This might contribute to the rapid binding of the transcription factors, such as DRE-binding protein (DREB)/C-repeat-binding factor (CBF) (Stockinger, Gilmour & Thomashow 1997; Liu et al. 1998) and ABRE-binding protein (AREB)/ABRE-binding factor (ABF) (Choi et al. 2000; Uno et al. 2000) in response to drought stress. The second type is that nucleosome density is gradually decreased in response to drought stress. This type is observed in RD20 and At2g20880 genes (Fig. 1).
Kwon et al. (2009) showed that the histone occupancy is decreased on the promoter regions of COR15A and ATGOLS3 genes in response to cold stress by the ChIP assay. The histone H3 occupancy did not change greatly after the return to normal growth temperature except for the promoter region of ATGOLS3. The histone H3 density in the ATGOLS3 promoter region increased in 1 d after the return and decreased in 3 d, suggesting that the changes in histone H3 occupancy might be coupled to the ATGOLS3 transcription.
Linker histone H1
Linker histone H1 is an important molecule to regulate the chromatin structure and gene activity (Izzo et al. 2008). Linker histone H1 binds to the linker DNA between nucleosome cores, thus facilitating the compaction of chromatin (Graziano et al. 1994; Ivanchenko, Zlatanova & van Holde 1997; Bassett et al. 2009). In Arabidopsis genome, there are three linker histone H1 homologs. Among them, the expression of HIS1-3 gene is induced by drought stress and ABA treatments (Ascenzi & Gantt 1997; Fig. 1; Table 1). The expression of the HIS1-3 gene was repressed in abi1 mutants subjected to the drought stress treatments. Analysis of transgenic plants containing the promoter:β-glucuronidase (GUS) fusion showed that HIS1-3 gene was highly expressed in root meristem and elongation zone of the drought-stressed young plants (Ascenzi & Gantt 1999). Fujita et al. (2005) showed that the expression of the HIS1-3 gene is up-regulated in plants over-expressing an activated form of AREB1 transcription factor encoding ABRE-binding protein. These results indicate that the HIS1-3 gene is a target one regulated by AREB1. Transgenic plants over-expressing the active form of AREB1 showed ABA hypersensitivity and enhanced drought tolerance.
A linker histone variant gene, HIS1-S, has been identified as a drought- and ABA-induced one in tomato (Scippa et al. 2000). Analysis of transgenic plants containing H1-S:GUS fusion showed that the H1-S protein accumulates in the nuclei and that it is associated with chromatin of wilted tomato leaves. H1-S antisense transgenic plants had a faster decrease in relative water content (RWC) of leaves compared with wild-type plants (Scippa et al. 2004; Table 1). Physiological analyses showed that stomatal conductance and transpiration rate were higher in the H1-S antisense transgenic plants than in wild-type plants, indicating that H1-S functions in regulating and modulating an important mechanism involved in the regulation of stomatal function.
The chromosomal HMG proteins are abundant and highly mobile chromatin-associated proteins that influence chromatin structure, and typically contain a central HMG-box DNA-binding domain (Grasser et al. 2007). In plants, proteins that belong to the HMGA and HMGB families containing AT-hook DNA-binding motifs and HMG-box domains, respectively, have been identified.
Over-expression of Arabidopsis HMGB1 protein decreased the seed germination rate under high-salinity stress conditions (Lildballe et al. 2008; Table 1). The seed germination in the presence of methyl methanesulphonate (MMS), a monofunctional DNA alkylating agent, was affected in both HMGB1-deficient lines and the over-expressors. Microarray analysis of the HMGB1-deficient lines showed that the stress-inducible genes, such as HIS1-3 and a LEA protein-encoding one, are down-regulated. The most significantly down-regulated gene ontology (GO) category was stress-responsive genes. No significant differences between HMGB1-deficient lines and wild-type in the overall chromatin structures were observed by the immunofluorescence experiments using antibodies against several histone H3 modifications, suggesting that HMGB1 does not affect changes in the histone H3 modification levels.
The expression of Arabidopsis HMGB2, HMGB3 and HMGB4 genes was up-regulated by cold stress, whereas the expression of the HMGB2 and HMGB3 genes was markedly down-regulated by drought or high-salinity stress (Kwak et al. 2007). Under high-salinity stress, the HMGB2-over-expressing Arabidopsis plants modulated the expression of several germination-responsive genes, and displayed retarded germination and subsequent growth compared with wild-type plants (Table 1).
The Arabidopsis HMGB1, HMGB2/3 and HMGB4 proteins are phosphorylated by casein kinase 2α (CK2α) (Stemmer et al. 2003), and the phosphorylation of the Drosophila HMG1 proteins by CK2 is important for their proper folding, stability and DNA-binding specificity (Wiśniewski et al. 1999). The phosphorylation of the HMGB proteins by CK2 might have a role in stress responses.
ATP-dependent chromatin remodeling factors
The switch (SWI)/sucrose non-fermenting (SNF) complex is a multisubunit DNA-dependent ATPase that contributes to the regulation of gene transcription by alteration of chromatin structure (Peterson & Workman 2000; Fry & Peterson 2001; Schwabish & Struhl 2007). The positions and/or structure of nucleosomes are altered by the SWI/SNF complex that can use the energy of ATP hydrolysis (Tsukiyama 2002).
Over-expression of AtCHR12, a SNF2/Brahma (BRM)-type chromatin remodeling factor in Arabidopsis, resulted in growth arrest of primary buds, as well as in reduced growth of the primary stems in response to drought and heat stress (Mlynárováet al. 2007, Table 1). On the other hand, the atchr12 knockout mutant shows less growth arrest than the wild type under stress. These results indicate that AtCHR12 plays a role in mediating the temporary growth arrest in response to the drought and heat stress.
A two-hybrid analysis revealed that SWI3B (Sarnowski et al. 2005), an Arabidopsis homolog of the SWI3 core subunit of SWI/SNF complex, is a prevalent partner of hypersensitive to ABA1 (HAB1), a protein phosphatase 2C playing a key role as a negative regulator of ABA signalling (Saez et al. 2008; Fig. 1; Table 1). The swi3b mutants showed a reduced sensitivity to ABA-mediated inhibition of seed germination and growth, and reduced expression of the ABA-responsive genes, such as RD29B and RAB18. ChIP assay showed that the presence of HAB1 in the vicinity of the ABA-responsive RD29B and RAB18 promoters is abolished by ABA. These results suggest that HAB1 modulates ABA response through the regulation of the SWI/SNF complex containing SWI3B.
The expression of PsSNF5 gene encoding a pea homolog of the SNF5 protein in the SWI/SNF complex was up-regulated by ABA and drought stress treatments (Rios et al. 2007). The yeast two-hybrid assay showed that PsSNF5 interacts with Arabidopsis AtSWI3A and AtSWI3B, suggesting that chromatin remodeling induced by PsSNF5-containing complex might contribute to the response to ABA and drought stress.
DNA methylation changes under stress conditions
DNA cytosine methylation, both asymmetric (mCpHpH, H is adenine, cytosine or thymine) methylation and symmetric (mCpG and mCpHpG) methylation, is associated with repression of gene transcription. De novo DNA methyltransferases domains rearranged methylase 1 (DRM1) and DRM2 catalyse new cytosine methylation, while the maintenance of symmetric CG and CHG methylation is mediated by the DNMT1-like enzyme MET1 and the plant-specific enzyme chromomethylase 3 (CMT3), respectively (Henderson & Jacobsen 2007).
Several reports showed that stresses can induce changes in hypomethylation of DNA. In tobacco, DNA methylation is reduced in the coding region of a glycerophosphodiesterase-like gene (NtGPDL) after aluminium, salt and cold stress treatments, and its reduction was correlated with the NtGPDL expression (Choi & Sano 2007). In maize roots, cold stress-up-regulated expression of ZmMI1 gene that contains part of the coding region of a putative protein and a retrotransposon-like sequence was correlated with the reduction of DNA methylation of the nucleosome core regions. In Arabidopsis, DNA methylation at the 180 bp centromeric repeat and other loci is reduced by infection with the bacterial pathogen Pseudomonas syringae (Pavet et al. 2006).