Search tips
Search criteria 


Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Integr Plant Biol. Author manuscript; available in PMC 2010 May 3.
Published in final edited form as:
PMCID: PMC2862557

Abscisic Acid-mediated Epigenetic Processes in Plant Development and Stress Responses


Abscisic acid (ABA) regulates diverse plant processes, growth and development under non-stress conditions and plays a pivotal role in abiotic stress tolerance. Although ABA-regulated genetic processes are well known, recent discoveries reveal that epigenetic processes are an integral part of ABA-regulated processes. Epigenetic mechanisms, namely, histone modifications and cytosine DNA methylation-induced modification of genome give rise to epigenomes, which add diversity and complexity to the genome of organisms. Histone monoubiquitination appears to regulate ABA levels in developing seeds through histone H2B monoubiquitination. ABA and H2B ubiquitination dependent chromatin remodeling regulate seed dormancy. Transcription factor networks necessary for seed maturation are repressed by histone deacetylases (HDACs)-dependent and PICKLE chromatin remodeling complexes (CRCs), whereas ABA induces the expression of these genes directly or through repression of HDACs. Abiotic stress-induced ABA regulates stomatal response and stress-responsive gene expression through HDACs and HOS15-dependent histone deacetylation, as well as through the ATP-dependent SWITCH/SUCROSE NONFERMENTING CRC. ABA also probably regulates the abiotic stress response through DNA methylation and short interfering RNA pathways. Further studies on ABA-regulated epigenome will be of immense use to understand the plant development, stress adaptation and stress memory.

Keywords: abiotic stress memory, abscisic acid, chromatin remodeling, DNA methylation, histone deacetylases

Abscisic acid (ABA) regulates plant growth and development such as germination, lateral root development, seedling growth, seed development, seed dormancy, transition from vegetative to reproductive phase and abiotic stress tolerance. Diverse roles of ABA in plants suggest the existence of multiple receptors and signal transduction pathways. Only recently three possible ABA-receptors, namely, FCA (flowering time control protein A) (Razem et al. 2006), ABAR (ABA receptor) similar to H subunit of Mg-chelatase (CHLH) (Shen et al. 2006) and G proteincoupled receptor (GCR2) (Liu et al. 2007a) have been identified. Although ABA signaling pathways are not yet thoroughly understood, it is very well established that most of the ABA responses (baring the quick stomatal closure response) are regulated by ABA-mediated transcriptional regulation, which have been extensively reviewed (Schroeder et al. 2001; Finkelstein et al. 2002; Zhu 2002; Chinnusamy et al. 2004; Nambara and Marion-Poll 2005; Yamaguchi-Shinozaki and Shinozaki 2006; Wasilewska et al. 2008). Recent discoveries reveal that besides genetic regulation, epigenetic regulation plays a key role in ABA-mediated plant processes. This review will briefly introduce the epigenetic processes, namely, histone modifications and cytosine DNA methylation, and further focus on the role of epigenetic processes in ABA-mediated developmental and stress response processes.

Epigenetic Processes

Epigenetics is defined as the study of changes in gene function that are mitotically and/or meiotically heritable, and that do not entail a change in DNA sequence (Wu and Morris 2001). Later, the definition included chromosomal marks that are transient as well as heritable (Bird 2007). Epigenetic modifications play pivotal roles in genomic imprinting (Feil and Berger 2007), paramutation (Alleman et al. 2006), defense against transposon proliferation (Vaucheret and Fagard 2001) and transcriptional gene silencing (Gong et al. 2002). Besides these phenomena, genomes are responsive to, and regulated by developmental and environmental cues through epigenetic processes.

Histone code

The basic unit of eukaryotic chromosome is the nucleosome, which consists of a histone-core complex (H2A, H2B, H3 and H4) wrapped around by 146 bp DNA and the linker histone H1 associated with the linker DNA (8 to 114 bp). Nucleosome structure depends on the histone variants and post-translational modifications in the N-terminal tails of core histones. The Arabidopsis genome encodes about 50 genes for histones (5 H1, 13 H2A, 11 H2B, 13 H3 and 8 H4). The N-tails of the core histones offer about 240 sites for post-translational modifications such as acetylation (Peterson and Laniel 2005), methylation (Shilatifard 2006), phosphorylation (Houben et al. 2007), biotinylation (Camporeale et al. 2007), ubiquitination (Sridhar et al. 2007), sumoylation (Nathan et al. 2006) and ADP-ribosylation (Hassa et al. 2006). Histone acetylation, phosphorylation, and ubiquitination activate transcription (Peterson and Laniel 2005; Houben et al. 2007; Sridhar et al. 2007), whereas biotinylation and sumoylation repress gene expression (Nathan et al. 2006; Camporeale et al. 2007). Dimethylation of H3 (K9 and K36) represses transcription, whereas trimethylation of H3K4 activates transcription (Zhang et al. 2007). Specific combinations of histone variants and core histones N-tail post-translational modifications called “histone code” offer enormous combinatorial possibilities for nucleosome assemblies. Histone code plays a key role in chromatin structure and affinity for chromatin-associated proteins, and thus regulates the expression of genetic code (Jenuwein and Allis 2001; Fuchs et al. 2006). Chromatin modification is induced by histone modification-dependent chromatin remodeling complexes (CRCs) and ATP-dependent CRCs (SWITCH/SUCROSE NON-FERMENTING, SWI/SNF complex) that non-covalently modify histones in the nucleosome (Fransz and de Jong 2002).

DNA methylation

Cytosine (5′) methylation of DNA is the ubiquitous mechanism of heritable epigenetic modification. DNA methylation maintains the methylated loci in a repressed state. In plants, asymmetric methylation (mCpHpH) is re-established after each mitosis cell division, whereas symmetric methylation (mCpG and mCpNpG) can be maintained across mitosis and meiosis divisions (Martienssen and Colot 2001). The de novo DNA methyltransferases catalyze new cytosine methylation, while maintenance DNA methyltransferases propagate the symmetric methylation marks on the parental DNA (Chan et al. 2005). The Arabidopsis bifunctional DNA glycosylase/lyase REPRESSOR OF SILENCING-1 (ROS1) actively removes DNA methylation by a base-excision repair mechanism (Gong et al. 2002; Agius et al. 2006), and thus has a key role in the plasticity of the epigenome (Zhu et al. 2007b). Arabidopsis DEMETER (DME), a protein similar to ROS1, is necessary for endosperm gene imprinting and seed viability in Arabidopsis (Choi et al. 2002). Post-translational modifications of histones and DNA methylation determine chromatin modeling and remodeling. These modifications can transmit epigenetic memory within one generation and across generations (Khorasanizadeh 2004; Vaillant and Paszkowski 2007).

ABA-mediated Epigenetic Processes in Seeds and Seedlings

Genetic analyses of ABA-deficient and ABA response mutants showed that ABA plays pivotal roles in storage reserve accumulation, desiccation tolerance, and dormancy of seeds and germination arrest. During seed development, two peaks of ABA accumulation were observed. Maternally-derived early peak of ABA is required for embryo maturation and prevention of vivipary. The embryo synthesizes the second peak of ABA accumulation in seed and this ABA appears to regulate dormancy, seed reserve accumulation and desiccation tolerance. Gene expression during seed development and germination inhibition are regulated by ABA through networks of transcription factors belonging to the B3 domain (ABI3, ABA INSENSITIVE3/VP1, VIVIPAROUS1; LEC2, LEAFY-COTYLEDON2; FUS3, FUSCA3), APETELA2 (ABI4), bZIP (ABI5) and HAP3 subunit of CCAAT binding factor (LEC1) (Finkelstein et al. 2002).

Seed maturation

Abscisic acid plays a central role in the accumulation of storage reserve and acquisition of desiccation tolerance during seed maturation. Seed storage protein accumulation requires a B3 transcription factor such as ALF (ABI3-like factor, Phaseolus vulgaris), ABI3 (in Arabidopsis), or VP1 (in Zea mays). The phaseolin (phas, encoding a major seed storage protein) gene is repressed in vegetative tissues and chromatin remodeling activates transcription of phas in seeds. PvALF1 transcription factor activates the ABA-dependent seed-specific expression of phas. Repression of phas expression is related to the deacetylated chromatin structure on phas promoter in leaves. DNase I foot printing assay revealed that the TATA boxes of phas are protected in the presence of both PvALF and ABA. ABA-induced expression of PvALF and the remodeling of chromatin architecture over the TATA box region of the phas promoter are required for phas expression (Li et al. 1999). Chromatin immunoprecipitation (ChIP) assay revealed that PvALF potentiates chromatin for transcription by mediating acetylation of H3-K9 and H4-K12 through histone acetyltransferases (HATs), whereas ABA has been shown to induce acetylation of H3-K14 and methylation of H3-K4 (Ng et al. 2006). Thus, chromatin remodeling in a euchromatin region plays a crucial role in ABA-induced gene expression.

Arabidopsis B3 domain transcription factors such as LEC2, FUS3, and ABI3 activate genes involved in the accumulation of storage proteins and lipids in the embryo during seed maturation. After completion of seed maturation, these genes are repressed in matured seeds and vegetative tissues. Arabidopsis pkl (pickle) and val (vp1/abi3-like) mutants exhibited derepression of embryonic genes in germinating seedlings (Ogas et al. 1999; Suzuki et al. 2007). The PICKLE (PKL) gene encodes a putative SWI/SNF-class chromatin-remodeling factor of the CHD3 type (harboring a Chromodomain, a SNF2-related helicase/ATPase domain, a DNA binding domain and a PHD zinc finger). VALs encode B3 proteins associated with chromatin factors. val1 val2 double mutant seedlings showed embryonic seedling phenotype, and upregulation of LEC1, ABI3, and FUS3 genes. It is suggested that VAL proteins repress the target genes by recruiting a chromatin-remodeling complex that includes PKL and related CHD3 proteins (Suzuki et al. 2007). Histone acetylation dependent chromatin remodeling also appears to regulate seed development as plant-specific hi-stone deacetylases (HDACs) such as HD2A, HD2B, and HD2C have been shown to express in ovules, embryos, shoot apical meristems, and primary leaves and is strongly induced during somatic embryogenesis in Arabidopsis (Zhou et al. 2004).

Seed dormancy

In natural ecosystems, plants complete their life cycle in favorable seasons and the seeds remain dormant during the unfavorable seasons. Thus, seed dormancy is crucial to avoid vivipary (pre-harvest germination of seeds on the mother plant) and germination of seeds under unfavorable conditions (Bewley 1997). Besides, successful agriculture also requires seed dormancy, as seeds harvested in the previous season need to be stored until the next season. Mutations that impair ABA biosynthesis (aba) and mode of action (abi1 to abi5, era1, sad1, abh1)also impair seed dormancy and germination under stress conditions. Molecular genetic analyses established the pivotal role of ABA, the original “dormin”, in inducing seed dormancy and prevention of germination. ABA is necessary for seed dormancy in many plants (Finkelstein et al. 2002) and tuber dormancy in potato (Suttle and Hultstrand 1994). However the mechanisms of dormancy and germination arrest are poorly understood. The ABA-mediated chromatin remodeling processes regulate some of the processes involved in seed dormancy and inhibition of germination under unfavorable conditions.

Treatment of potato tubers with bromoethane (BE, artificial breaker of dormancy) resulted in a decline of meristem ABA content due to reduction in the expression of StNCED (9-cis-epoxycarotenoid dioxygenase) and enhanced expression of StCYP707A1 and StCYP707A2 (ABA 8′-hydroxylases that catalyze inactivation of ABA) genes (Destefano-Beltrán et al. 2006). Expression pattern of these genes also showed a similar pattern during the ripening process in Arabidopsis seeds. Genetic analysis of Arabidopsis mutant, reduced dormancy4 (rdo4), which exhibits reduced seed dormancy, revealed a possible role of chromatin remodeling in seed dormancy through regulation ABA metabolism and response genes (Liu et al. 2007b).

The RDO4, which was named later as HISTONE MONOUBIQUITINATION1 (HUB1), encodes a C3HC4 RING finger E3 ligase that catalyzes histone H2B monoubiquitination. Mutation in HUB2, a homolog of HUB1, also reduced seed dormancy in Arabidopsis. hub1 and hub2 mutants are deficient in ubiquitinated H2B. Dormancy-related genes that are involved in ABA metabolism and response such as NCED9 and ABI4 showed reduced expression, whereas CYP707A2 showed enhanced expression in the freshly harvested seeds of hub1 mutant as compared with wild-type. Besides these genes, expression of DOG1 (DELAY OF GERMINATION 1), ATS2 (a caleosin-like protein) and PER1 (similar to the per-oxiredoxin family of antioxidants) were reduced in freshly harvested seeds of hub1 mutant. These expression patterns were similar to that of wild type after-ripened seeds (Liu et al. 2007b). Histone H2B monoubiquitination is associated with activation of gene transcription and deubiquitination is linked to repression (Sridhar et al. 2007). Hence, chromatin remodeling through HUB1 and HUB2 mediated H2B monoubiquitination plays a key role in seed dormancy (Liu et al. 2007b) probably by regulating ABA level in seeds, ABA sensitivity and other mechanisms.

Germination inhibition

Osmotic stress and salt concentration will be high during the non-rainy season and will decrease during the rainy season in salt-affected soils. In nature, scanty rainfall frequently occurs in non-rainy seasons with ensuing longer drought spells. If seeds germinate under these unfavorable conditions, then the chance for their survival is less. Hence, plants have impregnated adaptive mechanisms in seeds to prevent germination if osmotic stress occurs during the initial processes of germination. Exogenous application of ABA or osmotic stress within 48 h of imbibition can arrest or delay germination of Arabidopsis seeds. Germination arrest is mediated by induction and maintenance of ABI3 and ABI5 transcription factors expression. Chromatin remodeling is crucial for this germination arrest mediated by ABA and osmotic stresses. In Arabidopsis, The PKL (SWI/SNF type chromatin remodeling factor) expression is induced by imbibition and it mediates repression of embryonic traits during germination (Henderson et al. 2004; Li et al. 2005). During germination LEAFY COTYLEDON1, (LEC1, a transcriptional regulator that promotes embryonic identity) and FUSCA3 (FUS3) are repressed in wild type, whereas pkl mutants showed expression of LEC1 and FUS3 upon seed imbibition (Ogas et al. 1999). ABA has been shown to have a modest effect on the penetrance of pickle root phenotype (Henderson et al. 2004). Further, pkl mutants exhibit hypersensitive germination responses to ABA, and persistent high expression of ABI3 and ABI5 on ABA induction. ChIP studies comparing wild-type and pkl mutant seeds treated with or without ABA revealed ABA-treated pkl mutant seeds with 2.0–2.5-fold lower H3-K9 and H3-K27 methylation levels at ABI3 and ABI5 promoters than wild-type plants. Thus, chromatin remodeling mediated by PKL represses ABI3, ABI5 and some late embryogenesis abundant genes expression after imbibition to promote germination (Perruc et al. 2007).

Besides the histone methylation, histone deacetylation is also involved in ABA sensitivity during germination. Some of the histone deacetylases (HDACs) are induced by ABA in Arabidopsis (Sridha and Wu 2006) and rice (Fu et al. 2007). Impairment of expression of AtERF7 (APETALA2/EREBP-type transcription factor) showed a role for HDA19 in ABA sensitivity during seed germination. Arabidopsis ERF7 interacts with a global corepressor of transcription, AtSin3, which in turn interacts with HDA19. HDA19 and AtSin3 enhance the AtERF7 mediated transcriptional repression. RNA interference (RNAi) mediated suppression of AtERF7 and AtSin3 in transgenic plants and resulted in increased sensitivity to ABA during germination and seedling growth. ABA signaling appears to repress the genes through histone acetylation (Song et al. 2005). A transgenic HDA6-RNAi repression line treated with the HDAC inhibitor (trichostatin A) showed growth arrest and elevated expression of LEC1, FUS3, and ABI3 during germination. lec1, fus3, and abi3 mutants suppressed the growth-arrest phenotype of the HDA6-RNAi repression plants. The double repression line of HDA6/HDA19 displayed arrested growth after germination and the formation of embryo-like structures. These results suggest that HDA6 and HDA19 redundantly regulate the repression of embryonic properties and growth arrest during germination (Tanaka et al. 2008). In Arabidopsis, HDA6 has also been implicated in transgene silencing and the regulation of ribosomal RNA transcription (Probst et al. 2004; Earley et al. 2006). These lines of evidence suggest that histone deacetylation plays important roles in induction of embryonic genes and germination inhibition under unfavorable environments.

Epigenetic Processes in ABA-mediated Abiotic Stress Responses

The prominent role of ABA in abiotic stress adaptation of plants is well known. Stomatal regulation by ABA is crucial for regulation of transpiration and avoiding water-deficit stress in plants. ABA-mediated regulation of ion channels in guard cells is crucial for stomatal closure under unfavorable conditions. Calcium, protein kinases and phosphatases, and membrane trafficking components have been implicated in ABA signaling in guard cells (Schroeder et al. 2001). Similarly, calcium, protein kinases, protein phosphatases and transcription factor networks regulate expression of ABA-responsive genes and stress adaptation (Finkelstein et al. 2002; Zhu 2002; Chinnusamy et al. 2004; Yamaguchi-Shinozaki and Shinozaki 2006; Wasilewska et al. 2008).

Histone code regulates stomatal response

Histone variants offer a means to alter histone code. In tomato, the linker histone H1 variant, H1-S, was induced by drought through an ABA-dependent pathway (Bray et al. 1999; Scippa et al. 2000). This H1-S might be positively involved in drought tolerance by controlling transpiration as H1-S antisense tomato transgenic plants showed about 37% higher stomatal conductance, transpiration and photosynthetic rate than the wild type plants (Scippa et al. 2004). ABA might mediate stomatal response by chromatin remodeling through change in histone acetylation status at certain loci. Histone deacetylation also appears to regulate guard cells. Arabidopsis ERF7 interacts with AtSin3 and HDA19 to repress transcription of some genes. Transgenic Arabidopsis plants overexpressing AtERF7 show reduced sensitivity of guard cells to ABA, and increased transpirational water loss (Song et al. 2005). Further, ABA represses the expression of AtHD2C, and overexpression of AtHD2C resulted in a lower transpiration rate than that of the wild type plants (Sridha and Wu 2006). These results show that ABA-induced stomatal response mediated by chromatin remodeling plays a crucial role in stress tolerance.

ABA-mediated stress-responsive gene expression

Histone deacetylation results in a non-permissive chromatin conformation that represses transcription. Arabidopsis histone deacetylases HD2A, HD2B and HD2C have been implicated in transcriptional repression of genes (Wu et al. 2003). Expression analysis of rice HDAC genes revealed that the expression of several HDACs is influenced by plant hormones as well as abiotic stresses. ABA represses the expression HDT701, HDT702, SRT701 and SRT702 in rice. Abiotic stresses such as cold, manitol and salt also repress SRT701 and SRT702 (Fu et al. 2007). Abiotic stresses induce ABA accumulation, which in turn might repress the HDACs. In Arabidopsis, ABA represses the expression of AtHD2C. Transgenic Arabidopsis plants overexpressing AtHD2C exhibited ABA-insensitive phenotype as well as greater tolerance to salt and drought stresses than the wild type plants. The enhanced tolerance of transgenic plants constitutively overexpressing AtHD2C was partly due to increased expression of ABA-responsive LEA-like genes (RD29B and RAB18), and decreased expression of ABI2, ADH1 (alcohol dehydrogenase 1), SKOR (K+ outward rectifier), KAT1 and KAT2 (K+ inward rectifier) (Sridha and Wu 2006). These results show that ABA mediates abiotic stress responses through dynamic regulation of histone acetylation levels.

Further evidence for roles of histone acetylation in ABA and abiotic stress response was emerged from genetic analysis of hos15-1 (for high expression of osmotically responsive genes) mutant of Arabidopsis. An RD29A::LUC reporter-facilitated genetic screen led to the identification of the mutant hos15-1 mutant, which showed super-induction of RD29A::LUC in response to exogenous ABA, cold and salt stresses. hos15-1 mutants exhibit hypersensitivity to inhibition of germination by ABA and NaCl stress and also hyper-sensitive to freezing stress. HOS15 encodes a protein similar to the human WD-40 repeat protein TBL1 (transducin beta-like protein-1), a component of the chromatin repressor complex involved in histone deacetylation. ABA and abiotic stresses (cold, NaCl) enhanced the expression levels of HOS15. In Arabidopsis, HOS15 interacts with histone H4 and the level of acetylated histone H4 is higher in hos15 mutants as compared with that of the wild type. Under cold stress conditions, substantially higher levels of acetylated histone H4 are associated with higher expression levels of RD29A in the hos15 mutant than in wild type. Consistent with this, the induction of the RD29A gene is higher in the hos15 mutant than in the wild type under cold stress. Thus, ABA induces expression of HOS15 which in turn regulates ABA and abiotic stress responses through H4 deacetylation-dependent chromatin remodeling in Arabidopsis (Zhu et al. 2007a).

ATP-dependent CRCs also play a role in ABA-mediated stress responses. ABA and drought stress induce the expression of PsSNF5 (Pisum sativum SNF5), a CRC protein, in germinating embryos as well as vegetative tissues. PsSNF5 interacts with Arabidopsis SWI3-like proteins (SWI3A and SWI3B) in heterologous expression systems (Ríos et al. 2007). In yeast two-hybrid assay, AtSWI3A and AtSWI3B also interact with FCA, one possible ABA receptor (Sarnowski et al. 2005). Thus, ABA regulates the expression levels of PsSNF5, which in turn can mediate chromatin remodeling to regulate ABA-responsive gene expression (Ríos et al. 2007).

Regulation of DNA methylation by ABA

DNA methylation is associated with repression of gene expression, whereas demethylation leads to enhanced expression of genes (Zilberman et al. 2007). Cold stress induced DNA demethylation in maize (Steward et al. 2002). In tobacco, Aluminum, salt and cold stresses induced demethylation of the glycerophosphodiesterase-like protein (NtGPDL) gene, followed by upregulation of NtGPDL in leaves (Choi and Sano 2007). In tobacco cell-suspension culture, osmotic and salt stresses induced DNA hypermethylation in two heterochromatic loci, which was reversible when cells were returned to non-stress media (Kovarik et al. 1997). Water-deficit stress also induced specific cytosine hypermethylation (CCGG) in the pea genome (Labra et al. 2002). Although, ABA accumulation and the role of ABA in gene expression under abiotic stress are well known, the role of ABA in the DNA methylation/demethylation dependent gene expression is not understood.

H2B monoubiquitination (K143) regulates the methylation of histones H3 and deubiquitination of H2B directs CpNpG and CpNpN methylation. H2B deubiquitination by the nuclear ubiquitin protease SUP32/UBP26 is required for transcriptional gene silencing (TGS) (Sridhar et al. 2007). The HUB1 gene has been shown to monoubiquitinate histone H2B, which positively mediates ABA-induced seed dormancy, as bub1 mutation reduced the expression of NCED9 and ABI4, but enhanced the expression of CYP707A2 (Liu et al. 2007b). These results suggest a potential role of ABA-mediated processes such as stress response in addition to seed development.

Small RNAs

Non-coding regulatory small RNAs (~20–24 nt long) namely microRNAs (miRNAs) and small-interfering RNAs (siRNAs) have emerged as important players in plant development and stress responses (Jones-Rhoades et al. 2006; Sunkar et al. 2007). RNA-dependent RNA polymerases (RDR) play a crucial role in siRNA and miRNA biogenesis. AtRDR6/SGS2/SDE1 (RNA-dependent RNA polymerase6/SUPPRESSOR OF GENE SILENCING2/SILENCING DEFECTIVE1) catalyzes the synthesis of dsRNA from various RNAs derived from transgene, viral replication, natural antisense transcripts or miRNA-cleaved mRNA (Vazquez et al. 2004; Borsani et al. 2005; Wassenegger and Krczal 2006). OsRDR6 promoter contains an ABA-responsive DNA cis-element (ACGTG) at the −680 region and exogenous ABA application enhanced the OsRDR6 transcript level in rice cells grown on either acetate or sucrose. Further, ABA silences the isocitrate lyase (ICL) gene (a glyoxylate cycle enzyme) through the RDR6-generated siRNA(ICL) mediated post transcriptional gene silencing mechanism (Yang et al. 2008). Arabidopsis RDR2 is involved in transcriptional gene silencing (TGS) (Chan et al. 2004). Non-coding RNAs can also induce epigenetic changes through chromatin or DNA methylation (Bond and Finnegan 2007). Some ABA-induced small RNAs and RDRs can play a role in epigenetic regulation of abiotic stress response.

An endogenous siRNA identified from stress-treated Arabidopsis plants is complementary to At2g27152 (AAO3, a drought stress-inducible ABA biosynthesis enzyme). ABA and abiotic stresses have been shown to upregulate miR402. The predicted target of ABA-upregulated miR402 is At4g34060, which encodes a DNA glycosylase domain protein, DML3 (DEMETER-LIKE PROTEIN 3) similar to ROS1 (Sunkar and Zhu 2004). Two of the homologs of DML3 in Arabidopsis are involved in epigenetic regulation. The DMEDEMETER (DME) DNA glycosylase is required for endosperm gene imprinting and seed viability (Choi et al. 2002). The ROS1 DNA demethylase has a key role in the plasticity of the epigenome (Gong et al. 2002; Agius et al. 2006; Zhu et al. 2007b). It is probably that ABA-induced RDR6 might synthesize siRNA that target AAO3 and thus regulate the cellular levels of ABA under stress conditions. ABA-induced miR402 might reduce the transcript levels of DML3, which in turn can result in increases in methylation levels at certain loci and thus, repression of gene expression.

Abiotic Stress Memory

Abiotic stress-induced changes in the genome are necessary for stress memory. UV-C radiation or flagellin (an elicitor of plant defense) stress-induced changes in the genome have been shown to be a dominant trait and transmitted through both the maternal and the paternal crossing partner in Arabidopsis (Molinier et al. 2006). Progeny of tobacco mosaic virus (TMV) infected plants showed enhanced frequency of the somatic and meiotic recombination rates at certain loci due to DNA hypomethylation. Thus, stress memory appears to be inherited through epigenetic changes (Boyko et al. 2007). ABA accumulation in vegetative tissues is induced by abiotic stresses. ABA also enhances the somatic recombination frequency (Z Gong et al. unpubl. data, 2008). As discussed in this review, ABA induces chromatin remodeling. Chromatin remodeling regulates transcription, recombination, replication and genome organization (Meyer 2001). It is probably that ABA might also regulate DNA methylation through DML3 and siRNAs. Under abiotic stresses ABA mediates reduction in plant growth. One of the mechanisms of abiotic stress-induced growth arrest under abiotic stress is regulated by chromatin remodeling (Mlynárová et al. 2007). Abiotic stress-induced inheritable epigenetic state might have an adaptive advantage but also a negative effect on the yield of crops, as stress memory can inhibit the expression of full potential of crops. Hence it is imperative to understand the role of ABA in abiotic stress memory to use them for agricultural advantage.

Concluding Remarks and Perspectives

Abscisic acid regulates plant development and abiotic stress tolerance through genetic and epigenetic mechanisms. The role of ABA in epigenetic processes is just beginning to emerge (Figure 1). Seed development and germination are vital processes not only for plant survival but also for other organisms including humans, as successful agriculture depends on these processes. ABA plays a pivotal role in seed development and dormancy by direct induction of gene expression or histone ubiquitination, acetylation and methylation-dependent chromatin remodeling. In turn, these epigenetic processes might regulate ABA levels through change in the expression of genes involved in ABA metabolism. Transpiration, stomatal opening and plant growth are regulated under abiotic stresses through repression of histone deacetylation and chromatin modeling. ABA-regulated histone acetylation levels either through ABA-repression of histone deacetylases or repression of HOS15 (a protein similar to the human WD-40 repeat protein TBL1) plays a key role in chromatin remodeling, abiotic stress responsive gene expression and stress tolerance of plants (Figure 2). ABA also probably regulates siRNA pathways and DNA methylation under abiotic stresses. It is not known whether ABA-induced epigenetic changes in response to stresses are heritable through mitosis as well as meiosis and their adaptive advantage. Further studies on ABA-regulated epigenome will be necessary for better understanding of seed development, storage reserve accumulation in seeds, seed dormancy, plant development, abiotic resistance and engineering of these processes for agricultural use.

Figure 1
Abscisic acid (ABA) mediated epigenetic processes regulate seed maturation, dormancy and germination inhibition
Figure 2
Abscisic acid (ABA)-mediated chromatin remodeling regulates stress responsive gene expression and stress tolerance


Supported by SERC Fact Track Scheme for Young Scientist, DST, Govt. of India, New Delhi to V. Chinnusamy; the State Key Basic Research and Development Plan of China (2003CB114300) and the National Natural Science Foundation of China (30421002 and 30670182) to Z. Gong.


  • Agius F, Kapoor A, Zhu JK. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl. Acad. Sci. USA. 2006;103:11796–11801. [PubMed]
  • Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature. 2006;442:295–298. [PubMed]
  • Bewley JD. Seed germination and dormancy. Plant Cell. 1997;9:1055–1066. [PubMed]
  • Bird A. Perceptions of epigenetics. Nature. 2007;447:396–398. [PubMed]
  • Bond DM, Finnegan EJ. Passing the message on: inheritance of epigenetic traits. Trends Plant Sci. 2007;12:211–216. [PubMed]
  • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogeneous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell. 2005;123:1279–1291. [PMC free article] [PubMed]
  • Boyko A, Kathiria P, Zemp FJ, Yao Y, Pogribny I, Kovalchuk I. Transgenerational changes in the genome stability and methylation in pathogen-infected plants (Virus-induced plant genome instability) Nucleic Acids Res. 2007;35:1714–1725. [PMC free article] [PubMed]
  • Bray EA, Shih TY, Moses MS, Cohen A, Imai R, Plant AL. Water-deficit induction of a tomato H1 histone requires abscisic acid. Plant Growth Regul. 1999;29:35–46.
  • Camporeale G, Oommen AM, Griffin JB, Sarath G, Zempleni J. K12-biotinylated histone H4 marks heterochromatin in human lymphoblastoma cells. J. Nutr. Biochem. 2007;18:760–768. [PMC free article] [PubMed]
  • Chan SW, Henderson I, Jacobsen SE. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 2005;6:351–360. [PubMed]
  • Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303:1336. [PubMed]
  • Chinnusamy V, Schumaker K, Zhu JK. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J. Exp. Bot. 2004;55:225–236. [PubMed]
  • Choi CS, Sano H. Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol. Genet. Genomics. 2007;277:589–600. [PubMed]
  • Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell. 2002;110:33–42. [PubMed]
  • Destefano-Beltrán L, Knauber D, Huckle L, Suttle J. Chemically forced dormancy termination mimics natural dormancy progression in potato tuber meristems by reducing ABA content and modifying expression of genes involved in regulating ABA synthesis and metabolism. J. Exp. Bot. 2006;57:2879–2886. [PubMed]
  • Earley K, Lawrence RJ, Pontes O, Reuther R, Enciso AJ, Silva M, et al. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 2006;20:1283–1293. [PubMed]
  • Feil R, Berger F. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet. 2007;23:192–199. [PubMed]
  • Finkelstein R, Gampala S, Rock C. Abscisic acid signaling in seeds and seedlings. Plant Cell. 2002;14:S15–S45. [PubMed]
  • Fransz PF, deJong JH. Chromatin dynamics in plants. Curr. Opin. Plant Biol. 2002;5:560–567. [PubMed]
  • Fu W, Wu K, Duan J. Sequence and expression analysis of histone deacetylases in rice. Biochem. Biophys. Res. Commun. 2007;356:843–850. [PubMed]
  • Fuchs J, Demidov D, Houben A, Schubert I. Chromosomal histone modification patterns – from conservation to diversity. Trends Plant Sci. 2006;11:199–208. [PubMed]
  • Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell. 2002;111:803–814. [PubMed]
  • Hassa PO, Haenni SS, Elser M, Hottiger MO. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol. Mol. Biol. Rev. 2006;70:789–829. [PMC free article] [PubMed]
  • Henderson JT, Li HC, Rider SD, Mordhorst AP, Romero-Severson J, Cheng JC, et al. PICKLE acts throughout the plant to repress expression of embryonic traits and may play a role in gibberellin dependent responses. Plant Physiol. 2004;134:995–1005. [PubMed]
  • Houben A, Demidov D, Caperta AD, Karimi R, Agueci F, Vlasenko L. Phosphorylation of histone H3 in plants-a dynamic affair. Biochim. Biophys. Acta. 2007;1769:308–315. [PubMed]
  • Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293:1074–1080. [PubMed]
  • Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 2006;57:19–53. [PubMed]
  • Khorasanizadeh S. The nucleosome: from genomic organization to genomic regulation. Cell. 2004;116:259–272. [PubMed]
  • Kovarik A, Koukalová B, Bezdek M, Opatrn Z. Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor. Appl. Genet. 1997;95:301–306.
  • Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, et al. Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Boil. 2002;4:694–699.
  • Li G, Bishop KJ, Chandrasekharan MB, Hall TC. Betaphaseolin gene activation is a two-step process: PvALF- facilitated chromatin modification followed by abscisic acid-mediated gene activation. Proc. Natl. Acad. Sci. USA. 1999;96:7104–7109. [PubMed]
  • Li HC, Chuang K, Henderson JT, Rider SD, Jr, Bai Y, Zhang H, et al. PICKLE acts during germination to repress expression of embryonic traits. Plant J. 2005;44:1010–1022. [PMC free article] [PubMed]
  • Liu X, Yue Y, Li B, Nie Y, Li W, Wu WH, et al. A G proteincoupled receptor is a plasma membrane receptor for the plant hormone abscisic acid. Science. 2007a;315:1712–1716. [PubMed]
  • Liu Y, Koornneef M, Soppe WJJ. The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell. 2007b;19:433–444. [PubMed]
  • Martienssen RA, Colot V. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science. 2001;293:1070–1074. [PubMed]
  • Meyer P. Chromatin remodeling. Curr. Opin. Plant Biol. 2001;4:457–462. [PubMed]
  • Mlynárová L, Nap JP, Bisseling T. The SWI/SNF chromatin-remodeling gene AtCHR12 mediates temporary growth arrest in Arabidopsis thaliana upon perceiving environmental stress. Plant J. 2007;51:874–885. [PubMed]
  • Molinier J, Ries G, Zipfel C, Hohn B. Transgeneration memory of stress in plants. Nature. 2006;442:1046–1049. [PubMed]
  • Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Annu. Rev. Plant Biol. 2005;56:165–185. [PubMed]
  • Nathan D, Ingvarsdottir K, Sterner DE, Bylebyl GR, Dokmanovic M, Dorsey JA, et al. Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev. 2006;20:966–976. [PubMed]
  • Ng DWK, Chandrasekharan MB, Hall TC. Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell. 2006;18:119–132. [PubMed]
  • Ogas J, Kaufmann S, Henderson J, Somerville C. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc. Natl. Acad. Sci. USA. 1999;96:13839–13844. [PubMed]
  • Perruc E, Kinoshita N, Lopez-Molina L. The role of chromatin-remodeling factor PKL in balancing osmotic stress responses during Arabidopsis seed germination. Plant J. 2007;52:927–936. [PubMed]
  • Peterson CP, Laniel MC. Histones and histone modifications. Curr. Biol. 2005;14:R546–R551. [PubMed]
  • Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, et al. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcription gene silencing and determines nuclear organization of rDNA repeats. Plant Cell. 2004;16:1021–1034. [PubMed]
  • Razem FA, El-Kereamy A, Abrams SR, Hill RD. The RNA-binding protein FCA is an abscisic acid receptor. Nature. 2006;439:290–294. [PubMed]
  • Ríos G, Gagete AP, Castillo J, Berbel A, Franco L, Rodrigo MI. Abscisic acid and desiccation-dependent expression of a novel putative SNF5-type chromatin-remodeling gene in Pisum sativum. Plant Physiol. Biochem. 2007;45:427–435. [PubMed]
  • Sarnowski TJ, Ríos G, Jasik J, Swiezewski S, Kaczanowski S, Li Y, et al. SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development. Plant Cell. 2005;17:2454–2472. [PubMed]
  • Schroeder JI, Allen GJ, Hugouvieux V, Kwak JM, Waner D. Guard cell signal transduction. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2001;52:627–658. [PubMed]
  • Scippa GS, DiMichele M, Onelli E, Patrignani G, Chiatante D, Bray EA. The histone-like protein H1-S and the response of tomato leaves to water deficit. J. Exp. Bot. 2004;55:99–109. [PubMed]
  • Scippa GS, Griffiths A, Chiatante D, Bray EA. The H1 histone variant of tomato, H1-S, is targeted to the nucleus and accumulates in chromatin in response to water-deficit stress. Planta. 2000;211:173–181. [PubMed]
  • Shen YY, Wang XF, Wu FQ, Du SY, Cao Z, Shang Y, et al. The Mg-chelatase H subunit is an abscisic acid receptor. Nature. 2006;443:823–826. [PubMed]
  • Shilatifard A. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu. Rev. Biochem. 2006;75:243–269. [PubMed]
  • Song CP, Agarwal M, Ohta M, Guo Y, Halfter U, Wang P, et al. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses. Plant Cell. 2005;17:2384–2396. [PubMed]
  • Sridha S, Wu K. Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis. Plant J. 2006;46:124–133. [PubMed]
  • Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, et al. Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature. 2007;447:735–738. [PubMed]
  • Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 2002;277:37741–37746. [PubMed]
  • Sunkar R, Chinnusamy V, Zhu J, Zhu JK. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 2007;12:301–309. [PubMed]
  • Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell. 2004;16:2001–2019. [PubMed]
  • Suttle JC, Hultstrand JF. Role of endogenous abscisic acid in potato microtuber dormancy. Plant Physiol. 1994;105:891–896. [PubMed]
  • Suzuki M, Wang HHY, McCarty DR. Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol. 2007;143:902–911. [PubMed]
  • Tanaka M, Kikuchi A, Kamada H. The Arabidopsis histone deacetylases HDA6 and HDA19 contribute to the repression of embryonic properties after germination. Plant Physiol. 2008;146:149–161. [PubMed]
  • Vaillant I, Paszkowski J. Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 2007;10:528–533. [PubMed]
  • Vaucheret H, Fagard M. Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet. 2001;17:29–35. [PubMed]
  • Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, et al. Endogeneous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell. 2004;16:69–79. [PubMed]
  • Wasilewska A, Vlad F, Sirichandra C, Redko Y, Jammes F, Valon C, et al. An update on abscisic acid signaling in plants and more … Mol. Plant. 2008;1:198–217. [PubMed]
  • Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci. 2006;11:142–151. [PubMed]
  • Wu Ct, Morris JR. Genes, genetics, and epigenetics: a correspondence. Science. 2001;293:1103–1105. [PubMed]
  • Wu K, Tian L, Zhou C, Brown D, Miki B. Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J. 2003;34:241–247. [PubMed]
  • Yamaguchi Shinozaki K, Shinozaki K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 2006;57:781–803. [PubMed]
  • Yang JH, Seo HH, Han SJ, Yoon EK, Yang MS, Lee WS. Phytohormone abscisic acid control RNA-dependent RNA polymerase 6 gene expression and post-transcriptional gene silencing in rice cells. Nucleic Acids Res. 2008;36:1220–1226. [PMC free article] [PubMed]
  • Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu JK. Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE. 2007;11:e1210. [PMC free article] [PubMed]
  • Zhou C, Labbe H, Sridha S, Wang L, Tian L, Latoszek-Green M, et al. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J. 2004;38:715–724. [PubMed]
  • Zhu J, Jeong J, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, et al. Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proc. Natl. Acad. Sci. USA. 2007a;105:4945–1950. [PubMed]
  • Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr. Biol. 2007b;17:54–59. [PubMed]
  • Zhu JK. Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 2002;53:247–273. [PMC free article] [PubMed]
  • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 2007;39:61–69. [PubMed]