Sally Fitzgibbons Foundation

Beginning the Academic Essay

The molecular phenomena controlling gene expression is coordinated in the genome level where the availability of DNA sequences is determined by the structure called chromatin (van Dijk, Ding et al. 2010). Chromatin is a protein–DNA fibre containing a series of repeating nucleosome units. Each nucleosome is an octamer, containig two copies of each of the four core histone proteins (H2A, H2B, H3 and H4) with about 150 base pairs of DNA wrapped around it. This structure serves not just to bound or confine the DNA into the tiny space of the nucleus; it has also been incorporated to control gene expression by virtue of its capability to specifically make available or hide DNA sequences from DNA-binding proteins, which directly control gene expression (Deal and Henikoff 2010).
The organization of chromatin has a crutial role for the control of gene expression (Zhu, Dong et al. 2013) in different biological processes, including genome stability, recombination, developmental reprogramming, and reaction to external impulses. Alteration in histone variants, histone modifications and DNA methylation are usually regarded as epigenetic regulation. However, these changes may or may not possibly be truly epigenetic in nature considering common epigenetics definition encompass mitotic or meiotic heritability (Chinnusamy and Zhu 2009). H2A.Z is a conserved variant of histone H2A that is involved in many biological processes, such as transcriptional regulation, telomeric silencing, genome stability, cell cycle progression, DNA repair, and recombination (Sura, Kabza et al. 2017). Histone modification and ATP-dependent chromatin remodelling direct chromatin structure to harmonise chromatin packaging and transcriptional access (Qin, Zhao et al. 2014). H2A.Z influences many processes in fungi, plants and animals, including gene expression, recombination, and DNA repair (Xu, Leichty et al. 2018) H2A.Z is greatly enriched at the transcription start site (TSS) of a considerable set of genes across cell types, compatible with a role in the control or regulation of transcription, Genome-wide studies in yeast have revealed that H2A.Z enrichment at promoter-distal nucleosomes is needed for initiation or start of transcription, while being oppositely correlated with transcript levels (Sura, Kabza et al. 2017). Eukaryotic genomes possess several histone variants, and all of them bestow different properties to the nucleosome, which in turn influence many biological processes, most commonly and importantly transcription. Histones may also be altered post translationally and successively affect transcription (Dai, Bai et al. 2017).
The incorporation of H2A.Z directly to nucleosomes is conveyed through the SWR1 complex in plants that is made up of proteins encoded by ACTIN-RELATED PROTEIN 6 (ARP6), SWC6 and PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1) (Tasset, Yadav et al. 2018). massive rearrangement of transcription-associated with cell variation during development includes switch on and off of many genes (March-Diaz, Garcia-Dominguez et al. 2007). In plants, H2A.Z is associated to the response to turbulent temperature, the phosphate starvation response, osmotic pressure, the immune response, floral induction, female meiosis, recombination, thalianol metabolism, and the modulation of microRNA abundance (Qin, Zhao et al. 2014, Xu, Leichty et al. 2018). This task requires enormous rearrangement in chromatin assembly as it has been evidenced by the recognition of chromatin-remodeling factors whose mutation impairs regular development at multiple and different levels (March-Diaz, Garcia-Dominguez et al. 2007). Three most important biochemical methods or mechanisms have been described to alter chromatin configuration and assembly. The first requires the posttranslational covalent alteration of the amino- and carboxy-terminal ends of histones. The model of chemical alteration of histones within a nucleosome (acetylation, methylation, phosphorylation, ubiquitination, and SUMOylation) seems to constitute a code that can be interpreted by other nuclear machinery (March-Diaz, Garcia-Dominguez et al. 2007). Second is the ATP-dependent redirection of interactions between DNA and histones, which encompasses the distortion to the nucleosome assembly. The third medium of chromatin remodelling resides in the substitution of canonical histones of the octamer by histone variants, which confers evenness to the nucleosome (Mizuguchi, Shen et al. 2004, Kamakaka and Biggins 2005, March-Diaz, Garcia-Dominguez et al. 2007).


The Sick With Rat8 (SWR1) complex, a member of the Inositol requiring 80 (INO80) family of remodelers, mediates deposition of H2A.Z into nucleosomes. The SWR1 complex is unique in swapping H2A-H2B dimers for H2A.Z-H2B dimers (Qin, Zhao et al. 2014). SWR1-C is an evolutionarily conserved multi-protein complex first described in budding Yeast, three components of SWR1-C is essential for its function in yeast (Xu and Leichty 2018) The SWR1 complex (SWR1c) is an evolutionarily conserved Swi2/Snf2-related ATPase-containing chromatin remodelling complex that catalyzes the replacement of H2A by the histone variant H2A.Z in nucleosomes (Berriri, Gangappa et al. 2016). The ATPase, Swr1, provides the catalytic activity for the complex, and works in association with accessory proteins, Arp6 and Swc6. The orthologue of Swr1 in Arabidopsis is PHOTOPERIOD INDEPENDENT EARLY FLOWERING1 (PIE1); the orthologues of Arp6 and Swc6 are, respectively, ACTIN-RELATED PROTEIN6 (ARP6) and SERRATED LEAVES AND EARLY FLOWERING (SEF) (Wu, Alami et al. 2005). As in yeast, these proteins associate with each other, and loss-of function mutations in any of these proteins causes a significant decrease in H2A.Z (Wu, Alami et al. 2005, March-Diaz, Garcia-Dominguez et al. 2007, Xu and Leichty 2018). Several of the non-catalytic subunits including ACTIN-RELATED PROTEIN 6 (ARP6) and SWR1 COMPLEX 6 (SWC6) have been shown to be essential for histone replacement. ARP6, SWC6, and SWC2 act as a sub-complex, where the proteins are mutually essential for each other’s association and function within the complex. The components and function of SWR1c have been shown to be conserved in Arabidopsis (Wu, Alami et al. 2005, Berriri, Gangappa et al. 2016). Unlike the relatively simple two- to four-subunit composition of many ISWI complexes, the S. cerevisiae SWR1 complex contains up to fourteen distinct components, eight of which—Swr1, Swc2 (also called Vps72), Swc3, Swc5 (also called Aor1), Swc6 (also called Vps71), Swc7, Arp6, Yaf9 and Bdf1—are encoded by genes that are nonessential for cell viability. Other subunits of the complex—Act1 (actin), Arp4, Swc4 (also called God1), Rvb1 and Rvb2—are essential. Some of these have functions apart from the SWR1 complex or are shared components of the INO80 chromatin-remodeling complex and the NuA4 histone acetyltransferase complex, providing a basis for the mutant phenotype (Wu, Alami et al. 2005).

ATP-dependent chromatin remodelling complexes contribute to precise spatiotemporal transcription through distinct combinations of regulatory DNA sequences, DNA-binding transcription regulators, and chromatin-modifying enzymes. ATP-dependent chromatin remodeling complexes hydrolyze ATP and use the energy to exchange dimers of canonical histones in nucleosomes for dimers of histone variants (Qin, Zhao et al. 2014). The ATP-dependent SWR1 chromatin remodelling complex (SWR1-C) catalyzes the replacement of H2A-H2B dimers with H2A.Z-H2B dimers in nucleosome structures, thus producing variant nucleosomes with dynamic properties (Mizuguchi, Shen et al. 2004, Choi and Kim 2016). In eukaryotes, the organization of genomic DNA into chromatin and the ordered regulation of its accessibility to the transcription machinery are central to gene regulation. Mechanisms for regulation of chromatin structure include ATP-dependent chromatin remodeling as well as post-translational histone modifications. ATP-dependent chromatin remodeling complexes alter nucleosome composition and positioning, and thus can regulate DNA accessibility via chromatin compactness. Through its distinct physicochemical properties, H2A.Z influences nucleosome stability, and therefore chromatin structure, to modulate gene expression. These properties along with its incorporation into the chromatin out of mitosis have made H2A.Z central to transcriptional regulation underlying development and environmental responses. The components and function of SWR1c have been shown to be conserved in Arabidopsis. Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation (Berriri, Gangappa et al. 2016). H2A.Z is incorporated into chromatin via processes specifically catalyzed by multisubunit chromatin-remodeling complexes—SWR1 in yeast and the related SRCAP and Tip60 complexes in mammals (Liang, Shan et al. 2016). The yeast SWR1 enzyme contains fourteen subunits: the Swr1 ATPase, Swc2, Bdf1, Swc3, Arp6, Swc5, Yaf9, Swc6, and Swc7 subunits are encoded by genes not essential for cell viability; Rvb1, Rvb2, Arp4, Swc4 (also known as Eaf2), and Act1 are encoded by essential genes. Some subunits are not unique to the SWR1 complex and thus have functions apart from SWR1. For example, Rvb1, Rvb2, Act1, and Arp4 are shared components with another ATP-dependent chromatin remodeling complex INO80. Act1 and Arp4, along with Swc4 and Yaf9, are also shared with the histone acetyltransferase complex NuA4, Bdf1 interacts with TFIID at TATA-less promoters during RNA polymerase II transcription initiation. Deletion analysis of a number of nonessential SWR1 subunits has revealed that chromatin deposition of H2A.Z in vivo is dependent on Swc2, Arp6, Swc6, and Yaf9 as well as the Swr1 ATPase (Wu, Wu et al. 2009).
Three putative Arabidopsis SWR1 (At-SWR1) subunits have been identified and studied: PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX6 (SWC6) (Rosa, Von Harder et al. 2013), One of the mechanisms involved in chromatin remodelling is so-called ‘histone replacement’. An example of such a mechanism is the substitution of canonical H2A histone by the histone variant H2A.Z.(March-Diaz, Garcia-Dominguez et al. 2008). The SWR1 and SRCAP complexes facilitate ATP-dependent histone replacement of canonical H2A with the H2AZ variant in the nucleosome; this H2AZ histone exchange mechanism is a multistep process that uses the function of the SWR1 complex2 (Swc2), Swc6 and Arp6 subunits of the complex (Morrison and Shen 2009).
Gene functions are regulated by the modulation of chromatin structure as well as by the spatial association of genes with nuclear regions, including the nuclear lamina and the nucleolus. Chromatin remodeling complexes play central roles in the change of chromatin structure through their enzymatic activity and their regulatory subunits (Kitamura, Matsumori et al. 2015).
PIE1 is homologous to the yeast Swr1 and human SRCAP proteins. ARP6 and SEF are homologues of Arp6 and Swc6, two conserved subunits of the yeast SWR1 complex. Mutations in these three genes provoke early flowering due to down-regulation of FLOWERING LOCUS C (FLC), a MADS-box transcription factor that represses floral transition, Deal et al. (2007) have shown that PIE1 and ARP6 are required for deposition of H2A.Z at the FLC, MADS-AFFECTING FLOWERING 4 (MAF4) and MADS-AFFECTING FLOWERING 5 (MAF5) loci, suggesting that the PIE1/ARP6/SEF complex is functionally related to the yeast SWR1 complex (March-Diaz, Garcia-Dominguez et al. 2008).
The orthologue of Swr1 in Arabidopsis is PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1) (Xu, Leichty et al. 2018), Three components of SWR1-C are essential for its function in yeast. The ATPase, Swr1, provides the catalytic activity for the complex, and works in association with accessory proteins, Arp6 and Swc6 (Xu, Leichty et al. 2018) In the yeast SWR1 complex, ARP6 facilitates binding between other subunits, such as Swc2, and the ATPase domain of SWR1 (Qin, Zhao et al. 2014) Swc2 binds directly to and is essential for transfer of H2AZ. Swc6 and Arp6 are necessary for the association of Swc2 and for nucleosome binding, other subunits, Swc5 and Yaf9, are required for H2AZ transfer but neither H2AZ nor nucleosome binding (Wu, Alami et al. 2005). In budding yeast, ARP6 and SWC6 have been shown to be essential subunits in SWR1c for H2A.Z deposition. Along with SWC2, another component of the SWR1c in yeast, they act as a sub-complex that requires all three proteins for their association with the complex and for histone exchange (Mizuguchi, Shen et al. 2004, Wu, Alami et al. 2005, Berriri, Gangappa et al. 2016).

Genome integrity is constantly challenged both by environmental agents and by metabolic products that can induce DNA damage, The cellular response that follows, termed the DNA damage response (DDR), is a coordinated series of events that allows DNA damage detection, signaling (including cell-cycle checkpoint activation) and repair. In contrast with programmed events such as DNA replication in S phase, the DDR has to be elicited at any place and any time, where and when DNA lesions occur. Importantly, the DDR should not be considered just at the DNA level but also in the context of chromatin in eukaryotic cell nuclei, where DNA is wrapped around histone proteins (Soria, Polo et al. 2012). Damaged DNA needs to be repaired to prevent loss or incorrect transmission of genetic information (Adachi, Minamisawa et al. 2011). One of the most severe environmental challenges to cells is repair of DSBs, which can be caused by ionizing radiation (IR), environmental chemicals, or free radicals generated by cellular processes (Talbert and Henikoff 2014) The repair of DNA double-strand breaks (DSBs), induced by for example ionizing radiation or stalled replication forks, is essential for the maintenance of genomic integrity. Inefficient or inaccurate repair may result in DNA translocations or loss of genetic information, which in higher eukaryotes can lead to diseases such as cancer (van Attikum and Gasser 2005).
Damaged DNA needs to be repaired to prevent loss or incorrect transmission of genetic information. Eukaryotic DNA damage checkpoints delay or arrest the cell cycle to provide time for DNA repair before the cell enters a new round of DNA replication or mitosis (Adachi, Minamisawa et al. 2011). Two conserved mechanisms for DSB repair have evolved in eukaryotic cells. Homologous recombination (HR) retrieves and uses genetic information from an undamaged sister chromatid or homologous chromosome to seal the gap, while nonhomologous end-joining (NHEJ) involves the direct religation of DSB ends (van Attikum and Gasser 2005). These chromatin-remodeling complexes are ATP-driven molecular machines that slide, remove, and reconstruct nucleosomes, thus regulating gene transcription, DNA repair, homologous recombination, and many other nucleic acid transactions (Cao, Sun et al. 2016). Double-strand breaks (DSBs) are a particularly deleterious type of DNA damage, and their quick and efficient removal is of the utmost importance, as a single unrepaired DSB can be lethal to cells (Rosa, Von Harder et al. 2013) SWR1, with a known function in transcriptional regulation and histone variant deposition, has an additional role in facilitating DNA repair. This is evident from genetic, molecular, developmental, and cytological data documenting increased sensitivity to DNA damage, apparent DNA damage symptoms, decreased SHR, and meiotic defects in mutants lacking one of three subunits of the complex (Rosa, Von Harder et al. 2013) Studies on transcription have shown that this can be achieved in two ways; either by posttranslational modification of histone tail residues (phosphorylation, acetylation, methylation or ubiquitinylation) or by chromatin remodeling through the action of large ATP-dependent complexes(van Attikum and Gasser 2005) INO80 and SWR1 assist DSB repair. DSBs caused by genotoxic stress are particularly dangerous lesions that can result in mutations owing to error-prone repair or cell death if left unrepaired. The major pathways of DSB repair include homologous recombination (HR) and non-homologous end joining (NHej). The Mre11–Rad50–Xrs2 (MRX) complex, which contains exonuclease activity, collaborates with other factors to promote the production of single-stranded DNA, a process known as resection66. Repair and checkpoint factors, such as the Mec1 kinase, then localize to break sites. During HR, RAD52 epistasis group proteins (Rad50, Rad51, Rad52, Rad54 and Rad55) promote homology search, strand invasion and synapsis between the invading recipient strand and donor DNA, leading to the formation of Holliday junctions. DNA repair is complete once DNA synthesis has finished and Holliday junctions have been resolved. Alternatively, during NHej, the Ku70–Ku80 complex facilitates tethering and ligation of the broken DNA ends (Morrison and Shen 2009). Defects in the chromatin-remodelling activity of the INO80 subfamily complexes ultimately result in deficient DNA repair. For instance, mutants of the Arp subunits in the S. cerevisiae INO80 complex have defects in NHej as well as the HR pathway71. In arp8 mutants, when HR repair does occur, gene conversion often consists of large and discontinuous DNA tracts that might result from unstable heteroduplex DNA that forms during strand invasion and branch migration67. Indeed, mutants of the INO80 complex in plants and mammals also display defects in DSB repair suggesting conserved mechanisms for the INO80 complex in this pathway. By contrast, the S. cerevisiae Swr1 ATPase subunit does not seem to function in HR, but rather participates in the error-free NHej pathway. These results show that different complexes in the INO80 subfamily can contribute to distinct repair mechanisms, in part owing to the function of specialized subunits in each complex. Conversely, the yeast SWR1 complex does not affect nucleosome eviction at DSBs. However, deletion of its chromatin substrate HTZ1, which is transiently enriched at DSB sites, results in decreased production of singlestranded DNA and reduced association of Rad51 to DSB proximal regions. The SWR1 complex is also needed for efficient recruitment of Mec1 and Ku80 to DSBs, which are required for NHej. In addition, deletion of HTZ1 results in the inability of a persistent DSB to localize to the nuclear periphery, a rather enigmatic event that promotes DNA repair. SWR1 complexes outside of transcription are largely found in genome stability pathways, such as DNA repair, replication, telomere regulation and centromere stability (Morrison and Shen 2009) they contribute to early DNA damage signaling, DNA repair, fine-tuning and amplification of checkpoint signals, restoration of chromatin organization after repair, and, finally, turning off of checkpoint signals (Soria, Polo et al. 2012). Mutations in genes for Arabidopsis SWR1 complex subunits PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1, ACTIN-RELATED PROTEIN6, and SWR1 COMPLEX6 cause hypersensitivity to various DNA damaging agents. Double mutant analysis reveals that SWR1 is involved mainly in HR repair pathways (Rosa, Von Harder et al. 2013).


Shoot development in higher plants consists of a juvenile vegetative phase, an adult vegetative phase, and a reproductive phase, which differ in many morphological and physiological traits (Xu and Leichty 2018). The flowering of plants is regulated by many environmental stimuli and endogenous factors. The flowering of Arabidopsis is promoted by long days, gibberellins, and vernalization, but it can occur eventually even in the absence of environmental cues (Takada and Goto 2003). The transition from vegetative growth to flowering is perhaps the most important and highly regulated developmental transition in the life of an adult plant. The decision to make this transition is based on a variety of environmental and endogenous cues, including day length, temperature, nutrient status and the developmental state of the plant. These stimuli are sensed by one or more genetic pathways, which feed into a central regulatory module that controls the switch to flowering (Meagher, Kandasamy et al. 2007). It has also been reported that putative homologs of components of the ATP-dependent chromatin remodelling complexes are involved in the regulation of flowering time (Choi, Park et al. 2007), null mutations in ARP6 result in early flowering under both long- and short-day photoperiods (Meagher, Kandasamy et al. 2007) implicating ARP6 to be under photoperiod- independent control. ARP6 and PIE1 are both required for the deposition of H2A.Z into chromatin at FLC and the FLC homologous genes MADS AFFECTING FLOWERING4 (MAF4) and MAF5. Loss of H2A.Z from chromatin in arp6 and pie1 mutants results in reduced expression of FLC, MAF4, and MAF5 (Deal, Topp et al. 2007). This early flowering phenotype results from a drastic reduction in the expression of the flowering repressor gene FLC, indicating that ARP6 is normally required to promote the expression of FLC. As mentioned previously, yeast and mammalian ARP6 proteins function with the SWR1 and SRCAP complexes, respectively, which deposit the histone variant H2A.Z into chromatin. Arabidopsis ARP6 causes defects in prophase I of female meiosis, including aberrant centromere pairing and organization, loss of homologous chromosome pairing, and reduction in normal bivalents. The SWR1 complex is a likely candidate to regulate gene expression during meiosis. In Arabidopsis, mutations in SWR1 complex subunits, including ARP6, showed that the SWR1 complex is also involved in female meiosis (Rosa, Von Harder et al. 2013, Qin, Zhao et al. 2014). In the same way, mutations in putative orthologues of the yeast SWR1 complex, including EARLY IN SHORTDAYS 1/SUPPRESSOR OF FRIGIDA 3/ACTIN RELATED PROTEIN 6 (ESD1/SUF3/ARP6) (Choi et al., 2005; Deal et al., 2005; Martin-Trillo et al., 2006), the SWI/SNF ATPase PHOTOPERIOD INDEPENDENCE1 (PIE1) (Noh et al., 2003), and SEF (SERRATED AND EARLY FLOWERING)/AtSWC6 (Choi et al., 2007; March-Diaz et al., 2007) have been described recently (Lazaro, Gomez-Zambrano et al. 2008). Interestingly, mutations in the Arabidopsis homologs of two other components of this complex, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1 (PIE1) and SERRATED LEAVES AND EARLY FLOWERING (SEF), also cause early flowering owing to reduced FLC expression It was recently shown that ARP6 and PIE1 are required for deposition of H2A.Z at both ends of the FLC locus and related floral repressor loci, Furthermore, the ARP6, PIE1 and SEF proteins interact, Loss of H2A.Z from FLC chromatin in the arp6 and pie1 plants correlates with reduced FLC expression, indicating that plant H2A.Z can potentiate transcriptional activation, similar to its role in yeast. These observations suggest that the SWR1– SRCAP complex is conserved in plants and support a model in which ARP6- and PIE1-mediated deposition of H2A.Z is required for repression of flowering and maintenance of the vegetative growth phase (Meagher, Kandasamy et al. 2007). The molecular mechanisms regulating gene expression are coordinated at the genome level where the accessibility of DNA sequences is determined by the structure of chromatin (van Dijk, Ding et al. 2010). The SWR1 complex is a likely candidate to regulate gene expression during meiosis (Qin, Zhao et al. 2014). ARP6 is a subunit of the SWR1 complex, and the arp6 mutation results in depletion of H2A.Z from chromatin and leads to defects in plant reproductive development (Qin, Zhao et al. 2014, Dai, Bai et al. 2017) In addition, H2A.Z interacts with both PIE1 and AtSWC2, and knockdown of the H2A.Z genes by RNA interference or artificial microRNA caused a phenotype similar to that of esd1/suf3/arp6 (Lazaro, Gomez-Zambrano et al. 2008). In Arabidopsis, mutations in SWR1 complex subunits, including ARP6, showed that the SWR1 complex is also involved in female meiosis (Rosa, Von Harder et al. 2013, Qin, Zhao et al. 2014). ARP6 and PIE1 are required for the deposition of H2A.Z at multiple loci, including the FLOWERING LOCUS C (FLC) gene, a central repressor of the transition to flowering. Loss of H2A.Z from chromatin in arp6 and pie1 mutants results in reduced FLC expression and premature flowering, indicating that this histone variant is required for high-level expression of FLC (Deal, Topp et al. 2007). Mutations in Arabidopsis SWC6 (AtSWC6), SUPPRESSOR OF FRIGIDA 3 (SUF3) and PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1 (PIE1), homologs of SWC6, ARP6 and SWR1, respectively, caused similar developmental defects, including leaf serration, weak apical dominance, flowers with extra petals and early flowering by reduction in expression of FLOWERING LOCUS C (FLC), a strong floral repressor. Chromatin immune precipitation assays showed that AtSWC6 and SUF3 bind to the proximal region of the FLC promoter, and protoplast transfection assays showed that AtSWC6 colocalizes with SUF3. Protein interaction analyses suggested the formation of a complex between PIE1, SUF3, AtSWC6 and AtSWC2. In addition, H2AZ, a substrate of SWR1C, interacts with both PIE1 and AtSWC2. Finally, knockdown of the H2AZ genes by RNA interference or artificial microRNA caused a phenotype similar to that of atswc6 or suf3. These results strongly support the presence of an SWR1C-like complex in Arabidopsis that ensures proper development, including floral repression through full activation of FLC (Choi, Park et al. 2007).


Developmental and environmental signals can induce epigenetic modifications in the genome, and thus, the single genome in a plant cell gives rise to multiple epigenomes in response to developmental and environmental cues (Chinnusamy and Zhu 2009). Nucleosomes containing the alternative histone H2A.Z are essential to perceiving ambient temperature correctly (Kumar and Wigge 2010). Eukaryotic organisms must respond to environmental changes with changes in gene expression to survive. Al-though we often think of environmental responses in terms of whole-organism responses, including growth, movement, learning, homeostasis, and immunity, ultimately all of these involve changes in gene expression in the relevant nuclei of the organism, and hence involve changes to the epigenomic landscape that provide access to genes that are packaged in nucleosomes (Talbert and Henikoff 2014). Gene expression driven by developmental and stress cues often depends on nucleosome histone post-translational modifications and sometimes on DNA methylation (Chinnusamy and Zhu 2009). One mode of altering chromatin is through the deployment of histone ‘variants’, non-allelic paralogs of the four ‘canonical’ core histones (H2A, H2B, H3, and H4) that package the genome into nucleosomes at replication. Histone variants substitute for their canonical counterparts, thereby changing the properties of nucleosomes. In recent years, histone variants have been shown to be involved in several modes of environmental responses (Talbert and Henikoff 2014).
Plants frequently encounter unfavourable environmental conditions such as heat, cold, drought, and pathogen infections. There is growing evidence that stress responses in plants affect epigenetic regulation and require certain epigenetic regulators (Chinnusamy and Zhu 2009). Adaptive strategies of plants to cope with stress are complex and depend on the precise and timely regulation of stress-responsive gene networks (Chinnusamy, Zhu et al. 2007, Popova, Dinh et al. 2013). Sessile organisms such as plants continually sense environmental conditions to adapt their growth and development. Temperature varies both diurnally, which is important for entraining the clock, as well as seasonally, providing information for the timing of reproduction, Extremes of temperature represent a significant stress for plants and are a major factor limiting global plant distribution. The sensitivity of plants to small changes in temperature is highlighted by significant changes in flowering time and distributions of wild plants that have occurred in the last 100 years. We find that H2A.Z-containing nucleosomes represent the major node of regulation of the temperature transcriptome in plants. H2A.Z nucleosomes wrap DNA more tightly, which influences the ability of RNA polymerase (Pol) II to transcribe genes in response to temperature, suggesting a mechanism by which the transcriptome can be thermally regulated. Access of proteins to DNA wrapped around histones is mediated through local unwrapping events. Chromatin remodeling complexes have been implicated in stress responses (Mittler, Kim et al. 2006, Kumar and Wigge 2010, Probst and Mittelsten Scheid 2015) for example, UV, cold, and heat stress result in the reactivation of silent transgenes and endogenous transposable elements, albeit without the reduction of DNA methylation and repressive histone marks (Popova, Dinh et al. 2013) At increased temperatures or when contacts of the histone core with the DNA are weakened, nucleosomes display high uncatalyzed mobility (Bilokapic, Strauss et al. 2018) An additional important argument comes from the cytologically visible structural rearrangements of heterochromatin upon several types of stress within the nuclei of the model plant Arabidopsis thaliana. As similar alterations occur upon developmental transitions, it is likely that changes in nuclear organization have a functional connection with, or may even be a prerequisite for, stress responses. Drought, a drastic condition for plants and signalled through a pathway involving abscisic acid, is linked to chromatin changes. Often connected with dehydration is osmotic stress or salinity, also elucidating responses at the chromatin level. Extreme temperatures induce specific responses affecting chromatin configurations: cold stress and heat stress for higher plants and in algae, Light deficiency induces chromatin changes, signalled by light perception factors, Exposure to energy-rich radiation or chemically induced damage of DNA exerts chromatin changes, and at least one chromatin remodelling factor supports the efficiency of DNA repair (Probst and Mittelsten Scheid 2015). This idea led to the identification of the bHLH transcription factor PIF4 as a key regulator of thermomorphogenic phenotypes including hyponasty, hypocotyl and petiole elongation. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) has emerged as a critical player in regulating phytohormone levels and their activity. To control thermomorphogenesis, multiple regulatory circuits are in place to modulate PIF4 levels, activity and downstream mechanisms. Thermomorphogenesis is integrally governed by various light signalling pathways, the circadian clock, epigenetic mechanisms and chromatin-level regulation. In addition to epigenetic modifications, chromatin remodelling has a prominent role in thermomorphogenesis. ACTIN RELATED PROTEIN 6 (ARP6) controls H2A.Z-nucleosome incorporation into chromatin, and plants carrying mutations in ARP6 display several aspects consistent with a constitutive thermomorphogenic response, such as longer hypocotyls and petioles and a transcriptome profile typical for high ambient temperatures, even at lower growth tem¬peratures, This implies a role for H2A.Z-containing nucle¬osomes in thermal regulation of transcription, H2A.Z-nucleosomes are highly enriched at the beginning of genes at the +1 position, adjacent to the transcription start site. For some genes, such as HEAT SHOCK PROTEIN 70 (HSP70), it has been shown that the occupancy of the +1 H2A.Z-nucleosome is rate-limiting for expres¬sion. Consequently, HSP70 was more highly expressed in the arp6 background compared with wild type at low ambient temperatures. Based on these observations, it was hypothesized that the observed high-temperature-induced H2A.Z eviction may provide thermal information to the cell by allowing better accessibility for transcrip¬tional regulators that ultimately orchestrate thermomorphogenesis. H2A.Z eviction therefore seems to enable temperature-dependent expression for at least some and possibly many genes notably, however, arp6 mutants still show an increase in hypocotyl elongation at warmer tempera¬tures, suggesting that H2A.Z-nucleosomes themselves do not trans¬mit all temperature information. (Quint, Delker et al. 2016).
Delayed germination was observed for hta9 hta11, arp6, and pie1 mutants under control conditions suggesting that nucleosomal H2A.Z deficiency may affect seed germination (Sura, Kabza et al. 2017). Changes in nucleosome occupancy and in the levels of histone H3 tri-methylation (lysine 4) or acetylation (lysine 9, 14 or 27) during dehydration stress occurred at four inducible Arabidopsis genes. Dehydration stress induces biosynthesis of abscisic acid (ABA), which as a second messenger activates signalling cascades that trigger stomatal closure and altered gene expression via chromatin remodeling. In turn, ABA regulation is achieved through genetic and chromatin modification mechanisms. Thus, chromatin structure and chromatin modifications are emerging as critical factors in plants’ responses to environmental cues (van Dijk, Ding et al. 2010).
In repressive transcription states, Arabidopsis H2A.Z deposition may result in more stable nucleosomes that act as barriers to the access of RNA polymerase II. Indeed, Arabidopsis H2A.Z is highly detected in the environment-responsive genes under non-inductive conditions, suggesting that H2A.Z plays a direct negative transcriptional role of them. However, in highly active transcription state suggest that Arabidopsis SWR1-C makes nucleosomes less stable, thus promoting transcription Consequently, H2A.Z is rapidly evicted from the nucleosome during transcription, so that the detected H2A.Z level displays an anticorrelation with the transcript level, It is also possible that SWR1-C acts in concert with other active chromatin modifiers such as EFS and COMPASS to promote active transcription as seen in FLC gene. Although Arabidopsis SWR1-C is required to maintain the active transcription states of developmentally regulated genes, such as FLC and MIR genes, it is also required for the repressive transcription states especially of environmentally responsive genes. Not only the protein-coding genes, such as HSP70 and JAZs, but also some MIR genes, such as miR398 and miR408, may require SWR1-C for their basal repression prior to environmental induction Thus, SWR1-C may contribute to maintain the repressive transcription states for the environmentally induced genes (Choi and Kim 2016).


Plants respond to pathogens through a variety of defence systems, one of the best characterized responses involves direct or indirect interaction of the product of a plant resistance (R) gene with the product of a pathogen avirulence (avr) gene. This ‘gene-for-gene’ response system is mediated by an increase in the levels of salicylic acid (SA), which triggers a long-lasting systemic immunity to subsequent infections known as systemic acquired resistance (SAR). SAR is associated with the hypersensitive response (HR), characterized by apoptotic like cell death. A number of genome-wide transcriptome analyses have recently shown that SAR involves extensive reprogramming of transcription. Thus, SA mediates changes in the expression pattern of about 1000–2000 genes (induction or repression). Such a broad effect on gene transcription may be associated with extensive chromatin remodelling, which would require the involvement of specific chromatin remodelling complexes. Three main mechanisms of chromatin remodelling have been proposed so far. The first involves post-translational covalent modification of the N- and C-termini of histones (Jenuwein and Allis 2001, March-Diaz, Garcia-Dominguez et al. 2007). The second consists of ATPdependent reorganization of interactions between DNA and histones, which results in destabilization of nucleosome structure or position. The third mechanism of chromatin remodelling involves substitution of canonical histones in the octamer by histone variants, in a process known as histone replacement (March-Diaz, Garcia-Dominguez et al. 2007). SWR1c components have been proposed to be negative regulators of plant immunity with pie1, swc6, and hta9 hta11 mutants reported to display spontaneous cell death and enhanced resistance to virulent bacterial pathogens. SWR1c components play different roles in resistance to different pathogensLoss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistanceMutations in SWR1c components PIE1 and SWC6 or in H2A.Z have been reported to result in constitutive activation of defense responses, demonstrating their importance in biotic interactions as well. Loss of PIE1 and SWC6 but not ARP6, leads to impaired effector-triggered immunity (ETI). The arp6 and swc6 mutants phenocopied each other with characteristic early flowering and serrated leaves. This was consistent with the biochemical interaction of ARP6 and SWC6 in yeast, where their existence in the complex is mutually dependent. The severe growth defects in the pie1 mutant have been previously attributed to the derepression of immune responses characterized by spontaneous cell death and upregulation of defense genes. pie1, swc6, and hta9 hta11 mutants showed more macroscopic disease symptoms and increased susceptibility toward Pst DC3000 compared with the wild-type Col-0. However, the arp6 mutant showed increased resistance. SA-mediated defense is activated during interaction with biotrophic pathogens while jasmonic acid (JA)-mediated defense is active against necrotrophs and herbivores, pie1, swc6, and hta9 hta11 mutant plants showed impaired SA-mediated defense responses even though they accumulated a high level of the SA hormone in response to Pseudomonas infection.
Genes involved in systemic acquired resistance such as PR1, PR5, EDS5, and NIMIN1 were highly upregulated in pie1, arp6 mutant showed modest upregulation of all the above genes except for EDS5. The pie1 mutant displays upregulation of SA-responsive gene expression. SA is a key regulator of signaling networks involved in defense along with other hormones such as JA. SA- and JA-mediated defense responses are triggered in the plant depending on the nature of the pathogen. These two pathways act antagonistically to modulate defense responses. gene expression analyses have shown that genes involved in systemic acquired resistance such as PR1 and PR5 were derepressed in the SWR1c mutants and therefore showed increased basal expression of defense genes(Robert-Seilaniantz, Grant et al. 2011, Van der Does, Leon-Reyes et al. 2013, Berriri, Gangappa et al. 2016).
PIE1, SWC6, and H2A.Z are positive regulators of resistance in Arabidopsis against both biotrophic and necrotrophic pathogens. ARP6 is a negative regulator of defense against biotrophs. Depletion of PIE1, SWC6, and H2A.Z, not ARP6, in mutants led to increased susceptibility. This was rather intriguing given the antagonistic interaction between SA- and JA-mediated defences. The contrasting phenotypes of the mutants show that PIE1, SWC6, and H2A.Z, not ARP6 have a positive function in JA/ET-mediated defense(Berriri, Gangappa et al. 2016).
PIE1 acts at least at two levels: upstream of the SA signal controlling expression of the SA biosynthetic genes EDS5 and ICS1 and downstream of the SA signal regulating NPR1 targets. SA-dependent SAR pathway is partially or totally activated when function of the putative Arabidopsis SWR1-like complex is impaired (Jenuwein and Allis 2001).
This SWR1-C-mediated histone exchange can have both positive and negative effects on transcription for example, a mutation in a component of SWR1-C reduces the transcription rate of floral repressor genes FLC, MAF4, and MAF5, thus contributing to early flowering. This shows the positive role played by H2A.Z deposition in transcription. In contrast, negative effects of SWR1-C on transcription have been reported in genes involved in systemic-acquired resistance (SAR), jasmonate (JA)-mediated immunity, the P-starvation response (PSR), and genes that respond to high temperatures, such genes are de-repressed in the arp6 mutant under non-inductive conditions. Thus, the increased expression of SAR and PSR genes leads to a respective increase in pathogen resistance and root hair development in arp6. The dual transcriptional roles of SWR1-C may be a result of its cooperative activities with different transcription regulators such as chromatin modifiers, post translational modifications of H2A.Z and other histone variants, and DNA methylation, which generates broad and distinct ranges of nucleosome stability (March-Diaz, Garcia-Dominguez et al. 2008, Choi and Kim 2016)
The SWR1 Chromatin remodelling complex plays a vital role throughout the life cycle of a plant ranging from shoot and root development, Flowering, Stress tolerance, Plant immunity, DNA damage repair and so many aspects of plant development. In plant defence and Immunity, PIE1 acts at least at two levels: upstream of the SA signal controlling expression of the SA biosynthetic genes EDS5 and ICS1 and downstream of the SA signal regulating NPR1 targets (Jenuwein and Allis 2001) as well as systemic-acquired resistance (SAR), jasmonate (JA)-mediated immunity, the P-starvation response (PSR), and genes that respond to high temperatures. In vegetative phase of plant development the SWR1 complex is a likely candidate to regulate gene expression during meiosis. In Arabidopsis, mutations in SWR1 complex subunits, including ARP6, showed that the SWR1 complex is also involved in female meiosis (Rosa, Von Harder et al. 2013, Qin, Zhao et al. 2014). Similarly in DNA damage repair SWR1 is known to function in transcriptional regulation and histone variant deposition, with an additional role in facilitating DNA repair which can be achieved in two ways; either by posttranslational modification of histone tail residues (phosphorylation, acetylation, methylation or ubiquitinylation) or by chromatin remodeling through the action of large ATP-dependent complexes (van Attikum and Gasser 2005). Chromatin remodelling is the future research area that can be used to answer many unanswered questions in plant molecular biology.

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