Emerging functions of chromatin modifications in auxin biosynthesis in response to environmental alterations Vol (0123456789)1 3 Plant Growth Regulation https //doi org/10 1007/s10725 018 0453 x REVIE[.]
Plant Growth Regulation https://doi.org/10.1007/s10725-018-0453-x REVIEW PAPER Emerging functions of chromatin modifications in auxin biosynthesis in response to environmental alterations Bich Hang Do1 · Vu Thi Bach Phuong2 · Gia‑Buu Tran3 · Nguyen Hoai Nguyen4 Received: 31 May 2018 / Accepted: 12 November 2018 © Springer Nature B.V 2018 Abstract Auxin is one of the most important hormone groups in plants It has been documented to play various functions in plant growth and development In this phytohormone group, indole-3-acetic acid (IAA) is widely considered as a main natural auxin To date, many lines of evidence have revealed that the alterations of ambient environment such as light and temperature conditions can affect the IAA biosynthesis which consequently redirects the growth and development of the plants so that they can adapt to the new environmental conditions Current studies have shown the large impact of chromatin modifications in the regulation of eukaryotic gene expression Previous studies have elucidated different epigenetic factors in the regulation of auxin signaling pathway in the plants This review aimed to provide a precise and systemic overview of the chromatin modifications at the auxin biosynthesis gene loci, namely YUCCA(YUC) genes, and their effects on the expression of these genes Based on these emerging data, we propose different hypothetical models demonstrating the functions of epigenetic factors as well as chromatin modifications in the regulation of YUCgenes which can subsequently determine the auxin accumulation in the plants Keywords Auxin biosynthesis · Chromatin modifications · Environmental alterations · H2A.Z · IAA · PIF · YUCCA (YUC) Introduction From the first discovery during 1930s, auxin has been widely studied and documented to play various functions in plant growth and development such as embryogenesis, cell elongation, root growth, root gravitropism, hypocotyl elongation, * Nguyen Hoai Nguyen nguyen.nhoai@ou.edu.vn Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam Department of Plant Biotechnology and Biotransformation, Faculty of Biology‑Biotechnology, University of Science, Vietnam National University - Ho Chi Minh City, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam Department of Biotechnology, Institute of Biotechnology and Food‑technology, Industrial University of Ho Chi Minh City, 12 Nguyen Van Bao Street, Ward 4, Go Vap District, Ho Chi Minh City, Vietnam Faculty of Biotechnology, Ho Chi Minh City Open University, 97 Vo Van Tan Street, District 3, Ho Chi Minh City, Vietnam leaf morphology, flowering, and development of flowers and fruits (Rayle and Cleland 1992; Collett et al 2000; Aloni et al 2006; Fukaki and Tasaka 2009; Scarpella et al 2010; Peer et al 2011; Mashiguchi et al 2011; Petricka et al 2012; Enders and Strader 2015; Velasquez et al 2016; HernándezMadrigal et al 2018) Generally, auxin is biosynthesized at the shoot and can be polarly transported to root via different pathways (Peer et al 2011; Enders and Strader 2015) Besides, some studies have elucidated that auxin can be also locally biosynthesized to regulate plant growth in response to different environmental changes (Ikeda et al 2009; Pinon et al 2013; Chen et al 2016; Liu et al 2016) Because of its crucial functions in the regulation of plant growth and development, the biosynthesis of auxin is regulated and/or influenced by many endogenous and exogenous factors (Brumos et al 2014; Enders and Strader 2015; Kasahara 2016) The changes of growth environment can effectively alter the auxin biosynthesis to redirect the growth and development of the plants so that they adapt to the new conditions For examples, after the seed germination, seedlings need to grow out from the soil so that they can use their leaves to catch the sunlight for photosynthesis During this time, the hypocotyl 13 Vol.:(0123456789) elongation is one of the critical developmental programs and this can be precisely regulated by ambient light and temperature conditions Many lines of evidence have indicated that shade conditions and warm ambient temperature can increase the auxin accumulation in plant resulting in hypocotyl elongation (Gray et al 1998; Tao et al 2008; Stavang et al 2009; Franklin et al 2011; Sun et al 2012; Hornitschek et al 2012; Muller-Moule et al 2016; Peng et al 2018) These environmental factors may employ different transcription factors such as PHYTOCHROME INTERACTING FACTOR (PIF4), PIF5, and PIF7 to activate the auxin biosynthesis genes including different YUCs resulting in the increased auxin accumulation (Tao et al 2008; Stavang et al 2009; Franklin et al 2011; Sun et al 2012; Hornitschek et al 2012; Muller-Moule et al 2016; Peng et al 2018) Current studies have shown the important functions of chromatin modifications in the regulation of gene expression in eukaryotic cells including the plant cells A number of studies have investigated the functions of different epigenetic mechanisms, such as histone acetylation, in the auxin signaling pathway (Manzano et al 2012; Nguyen et al 2013; Weiste and Droge-Laser 2014; Yamamuro et al 2016) In a previous review, Yamamuro et al (2016) comprehensively described the involvements between epigenetic modifications and the plant hormone action Particularly, the review highlighted the roles of the epigenetic modifications in the auxin signaling and distribution (Yamamuro et al 2016) It also mentioned the possible function of histone H3 methylation, namely H3K27me3, in the regulation of different auxin biosynthesis genes including YUCs (Yamamuro et al 2016) Here, based on the emerging results, this review aims to provide an overview and some hypotheses of the environmental effects on chromatin modifications which can influence the expression of different YUCs resulting in altering the auxin biosynthesis Chromatin modifications and gene expression Nucleosome occupancy In the nuclei of eukaryotic cells, genomic DNA and histone proteins assemble to comprise a structure called nucleosome which is considered as a basic element of chromatin Generally, about 145–147 bp of DNA wraps around a protein core composed of eight proteins including one pair of each: H2A, H2B, H3, and H4 protein (Mellor 2006; McGinty and Tan 2015; Lai and Pugh 2017) The interaction between DNA and histone proteins can determine the gene transcription as well as DNA replication (Mellor 2006; McGinty and Tan 2015; Lai and Pugh 2017) Since nucleosomes can negatively influence the passage of RNA polymerase II (RNAPII) 13 Plant Growth Regulation through the gene body, their positioning critically affects the gene transcription (Workman 2006; Kulaeva et al 2013) In order to induce a certain gene, the given nucleosomes might be moved/evicted to generate nucleosome-free gaps and this process may also be involved in the competition between nucleosomes and transcription factors (Workman 2006; Struhl and Segal 2013; Zhang et al 2015) Histone acetylation and methylation The histone post-translational modifications or replacement of their sequence variants can also alter the strength of DNA–histone core interaction which consequently influences the gene expression and DNA replication (Bannister and Kouzarides 2011; Kim et al 2015; Lai and Pugh 2017) A number of histone modifications have been documented such as methylation, acetylation, phosphorylation, sumoylation, or ubiquitination (Strahl and Allis 2000; Kim et al 2015) The histone acetylation and deacetylation are respectively catalyzed by histone acetyltransferase (HAT) and histone deacetylase (HDA) enzymes In Arabidopsis, 12 HATs and 18 HDAs have been identified (Pandey et al 2002; Hollender and Liu 2008; Yuan et al 2013) In addition, several histone methyltransferases and histone demethylases (HDMs) have been isolated in Arabidopsis (Kim et al 2015) In general, histone acetylation (H3ac and H4ac) is considered as gene activation marker while the histone methylation exhibits the inconsistent effects on gene expression (Dong and Weng 2013; Kim et al 2015; Lawrence et al 2016) For instance, the trimethylation of lysine on histone H3 (H3K4me3) is associated with gene activation whereas the trimethylation of lysine or 27 on histone H3 (H3K9me3 or H3K27me3) is gene silencing marker (Kim et al 2008, 2015; Kwon et al 2009; Lawrence et al 2016) Histone H2A.Z As we mentioned above, the histone proteins can be replaced by their sequence variants to remodel the chromatin structure (Lai and Pugh 2017) Many lines of evidence have shown the important functions of histone H2A.Z, a variant of H2A protein, in plant growth and development (To and Kim 2014; Jarillo and Pineiro 2015) Based on the genomewide analyses, an interesting concept mentioning the relationship between DNA methylation and H2A.Z-containing nucleosome occupation was proposed These studies showed that the gene bodies with high DNA methylation levels were found to prohibit the incorporation of H2A.Z and vice versa (Zilberman et al 2008; Coleman-Derr and Zilberman 2012) In the yeast cells, the chromatin remodeling SWR1 complex is considered to deposit H2A.Z-containing nucleosomes to a certain genome region while the INO80 complex exchanges the H2A.Z by H2A proteins Plant Growth Regulation (Papamichos-Chronakis et al 2011; Weber and Henikoff 2014; Brahma et al 2017; Lademann et al 2017) In Arabidopsis, different SWR1 chromatin-remodeling complex subunits have been characterized such as ACTIN-RELATED PROTEIN6 (ARP6), PHOTOPERIOD-INDEPENDENT EARLY FLOWERING (PIE1), SWR1 COMPLEX6 (SWC6), and SWC2 (Noh and Amasino 2003; Choi et al 2005, 2007; Deal et al 2007) The replacement of H2A by H2A.Z protein can either activate or repress the transcription of various genes (Kumar and Wigge 2010; Deal and Henikoff 2011; To and Kim 2014; Sura et al 2017; Nguyen and Cheong 2018) In fact, FLOWERING LOCUS C (FLC) expression is significantly reduced in arp6-1 and pie1-5 mutants along with the decreasing of H2A.Z levels at this gene locus (Deal et al 2007) On the other hand, the transcript levels of different Pi STARVATION RESPONSE (PSR) genes are increased in arp6-1 mutant while the enrichment of H2A.Z is decreased at these gene loci (Smith et al 2010) Moreover, this histone variant H2A.Z was confirmed to modulate the transcription of various temperature or drought stress-responsive genes in both ways (up- or down-regulation) (Kumar and Wigge 2010; Sura et al 2017) From these results, we can realize that H2A.Z-containing nucleosomes can either positively or negatively affect gene transcription Kumar and Wigge (2010) proposed that the occupation of H2A.Z-containing nucleosomes can physically disturb the targeting of RNAPII or transcription activators leading to the reduction of transcription, and they can also prevent the activity of repressors which can bind and suppress the expression of target genes during the deportation of these H2A.Z-containing nucleosomes DNA methylation Being different from mammalian genomic DNA, the cytosine in plant DNA can be methylated at three different sequence contexts including CG, CHG, and CHH (H could be A, T, or C) (Saze et al 2012; Kim et al 2015) The DNA methylation is reversible and regulated by different pathways including de novo methylation, maintenance methylation, and active demethylation (Kim et al 2015) Previous studies in Arabidopsis unraveled that the environmental alterations can trigger the changes in DNA methylation status of different genes such as SPEECHLESS, FAMA, and AtMYB74 (Tricker et al 2012; Xu et al 2015) The transcript levels of two genes, SPEECHLESS and FAMA, are decreased in response to low relative humidity which can trigger the cytosine methylation within these genes via the RNA-directed DNA methylation pathway (Tricker et al 2012) Besides, the salt stress was found to induce the AtMYB74 expression in association with the reduction of DNA methylation at this gene promoter region (Xu et al 2015) These studies support that DNA methylation is associated with gene silencing However, some emerging studies have found that the body of highly transcribed genes could be methylated or the DNA methylation is even involved in gene activation (Zilberman et al 2008; Siegfried and Simon 2010; Zemach et al 2010; Halpern et al 2014; Kim et al 2015; Grzybkowska et al 2018) YUCs function in auxin biosynthesis and the influences of environmental factors on these genes expression In Planta, the first identified hormone is auxin and indole3-acetic acid (IAA) is one of main natural auxin that was discovered in the 1930s (Mashiguchi et al 2011) Although the IAA functions as one of most important plant hormone compounds, IAA biosynthesis is still not understood entirely, and this is caused of the multiple biosynthesis pathways and functional redundancy of enzymes within the pathway (Mashiguchi et al 2011) There are two main pathways of IAA biosynthesis including tryptophan-dependent and tryptophan-independent pathways (Zhao 2010; Kasahara 2016) Basically, tryptophan is considered as the main precursor of IAA biosynthesis and this tryptophan-dependent pathway has been well characterized (Zhao 2010; Mashiguchi et al 2011; Kasahara 2016) Based on various genetic and biochemical evidence, the tryptophan-dependent IAA biosynthesis pathway is proposed to contain four distinguished branch ways: (1) the indole-3-acetamide (IAM), (2) the indole-3-acetaldoxime (IAOx), (3) the indole-3-pyruvic acid (IPA), and (4) the tryptamine (TAM) (Fig. 1) (Zhao 2010; Mashiguchi et al 2011; Kasahara 2016) The YUC enzymes function in the pathway (3) and catalyze the reaction to transform the IPA to IAA (Fig. 1) (Mashiguchi et al 2011) A number of studies have suggested that the pathway through the YUC enzymes is a common pathway in auxin biosynthesis (Cheng et al 2006; Yamamoto et al 2007; Mashiguchi et al 2011) A previous study proposed that the reaction (from IPA to IAA) catalyzed by YUCs is the ratelimiting step in the auxin biosynthesis (Zhao et al 2001) Since YUCs function critically in auxin biosynthesis, this review mainly focuses on the influences of environmental changes on YUCs expression which can subsequently affect the auxin accumulation In Arabidopsis, there are 11 YUC genes encoding FLAVIN MONOOXYGENASE-LIKE enzymes which catalyze an important step in auxin (IAA) biosynthesis pathway (Cheng et al 2006; Zhao 2010; Mashiguchi et al 2011; Kasahara 2016) Overexpression of YUCs can lead to increase the endogenous auxin levels as well as the high auxin phenotypes Kim et al (2007) showed that YUC6overexpression (yuc6-1D) plants have high auxin levels and 13 Fig. 1 The simple tryptophan-dependent pathway of IAA biosynthesis in plant From the tryptophan, IAA can be biosynthesized via four different branch ways: (1) the indole-3-acetamide (IAM), (2) the indole-3-acetaldoxime (IAOx), (3) the indole-3-pyruvic acid (IPA), and (4) the tryptamine (TAM) This simple tryptophan-dependent pathway of IAA biosynthesis was drawn based on a previous study (Mashiguchi et al 2011) exhibit the overproduction auxin phenotypes such as long hypocotyl, epinastic cotyledons, increased apical dominance, curled leaves, and extremely tall inflorescences Moreover, the overexpression of two genes YUC8 and YUC9 also resulted in the high endogenous auxin levels as well as the similar phenotypes to those exhibiting in yuc6-1D plants (Hentrich et al 2013; Kim et al 2007) Despite the overexpression of a single YUCgene can cause the overproduction auxin phenotypes, the knock-out of only one YUCgene does not show the obvious phenotype implying that these YUCs can be functionally redundant in the plant cells (Di et al 2016) A number of studies have documented that the transcript accumulation of YUC genes is regulated by different environmental factors such as light conditions, ambient temperature, and stress signals (Table 1) The low red: far red light conditions (to mimic the shade conditions) can increase the transcript levels of YUC2, 5, 8, and (Tao et al 2008; Hornitschek et al 2012; Muller-Moule et al 2016; Peng et al 2018) The warm ambient temperature (28–29 °C) was shown to induce the endogenous IAA levels in association with the increased transcript levels of different genes (TAA1, CYP79B2, and YUC8) involving in auxin biosynthesis (Franklin et al 2011; Sun et al 2012) The transcription factor PIF4 was found to directly target and induce the expression of these genes in response to warm temperature (Franklin et al 2011; Sun et al 2012) In addition, Hwang et al (2017) also found that the PIF4 may indirectly control the auxin biosynthesis gene (YUC8) expression via its downstream genes including LONGIFOLIA1 (LNG1) and 13 Plant Growth Regulation LNG2 under warm-growth conditions A previous study has proposed that the aluminum stress triggers the local ethylene levels resulting in up-regulation of TAA1 and YUCs to induce the auxin levels and modify the root development to optimize the plant growth under this stress condition (Liu et al 2016) Different YUCgenes were found to quickly increase their transcript levels in response to wound signal(s) (Chen et al 2016) Besides, the wound may generate different physical and chemical signals including the plant hormone jasmonate (JA; Leon et al 2001; Koo and Howe 2009; Chen et al 2016) In addition, Hentrich et al (2013) found that the methyl jasmonate (MeJA) treatment can induce the expression of YUC8 and YUC9 demonstrating the link between jasmonic acid (JA) signaling and auxin homeostasis These data indicate that wounding stress may increase the JA signals leading to induce the YUCs expression to modify the local auxin levels and cell differentiation (Chen et al 2016; Hentrich et al 2013; Koo and Howe 2009) Chromatin modifications influence YUCs expression under environmental alterations Expression of YUC genes is associated with histone acetylation As we mentioned above, shade conditions were shown to induce the transcript levels of several YUCgenes including YUC2, 5, 8, and (Hornitschek et al 2012; Muller-Moule et al 2016; Peng et al 2018) A number of light-related transcription factors have been found to directly or indirectly regulate the expression of these YUC genes in response to various light conditions In a previous study, Kwon et al (2013) investigated a novel transcription factor called MYBH which is involved in the regulation of the hypocotyl elongation The transcript levels of this MYBH gene are controlled by light conditions and MYBH-overexpression plants (MYBH-OX) exhibit the obvious long hypocotyl phenotype in association with the increased endogenous auxin levels Moreover, the YUC8 and other genes such as PIF4 and PIF5 were found to be induced in MYBH-OX plants Because of the lacking of MYBH-targeted genes analysis, this study only proposed that MYBH may directly induce YUC8 or just indirectly promote this gene expression mediating by the PIF4 and PIF5 transcription factors (Kwon et al 2013) In fact, the expression of these YUC genes in response to shade conditions is dependent on different PIF transcription factors such as PIF4, PIF5, and PIF7 (Hornitschek et al 2012; Peng et al 2018) Currently, Peng et al (2018) have proposed a delicate mechanism which showed that PIF7 interacts with the H3K4me3/H3K36me3-binding protein, MORF RELATED GENE (MRG2) to target and induce their downstream genes such as YUC8 and IAA19 which are Increased expression in response to aluminium stress (this is ethylene dependent) Increased expression in H3K4me2/3: gene body response to shade treatH3K27me3: gene body (TSS ment (low red:far red proximal) and promoter conditions);to aluminium (~ 0.5 kb of upstream region) stress (this is ethylene dependent); to darkness H3K4me2/3: gene body Increased expression in H3K27me3: gene body response to shade treatment (low red:far red conditions); to aluminium stress (this is ethylene dependent); to darkness H3K27me3: gene body (TSS proximal) and first exon H3K4me2: TSS proximal H3K27me3: gene body (TSS proximal) and promoter (up to ~ 1.5 kb of upstream region) Increased expression in response to shade treatment (low red:far red conditions); to aluminium stress (this is ethylene dependent); to darkness Increased expression in response to wounding Increased expression in response to shade treatment (low red:far red conditions) Increased expression in response to aluminium stress (this is ethylene dependent) Increased expression in response to wounding Environmental factors H4K5ac, H3K9ac, and H3K27ac were increased in response to shade conditions H3K27me3 was decreased in response to wound signal H3K27me3 was decreased in response to wound signal Histone modifications (*) DNA methylation and H3K4 and/or H3K27 methylation status at YUC loci (the data was extracted from http://epiqenomics.mcdb.ucla.edu) AT1G48910 YUCCA10 Promoter (from ~ 1 kb to upstream region) AT1G04180 YUCCA9 AT4G28720 YUCCA8 AT2G33230 YUCCA7 AT5G25620 YUCCA6 AT5G43890 YUCCA5 AT5G11320 YUCCA4 AT4G13260 YUCCA2 Promoter (~ 2.5 kb of upstream H3K4me1/2: gene body region) H3K27me3: promoter (~ 0.5 kb) H3K4me2: TSS proximal H3K27me3: gene body and promoter (from ~ 1 kb to upstream region) Promoter (~ 2.5 kb of upstream H3K4me2: gene body region) H3K27me3: gene body and promoter (up to ~ 1 kb of upstream region) H3K4 and/or H3K27 methylation status (*) AT1G04610 YUCCA3 DNA methylation (*) H3K27me3: gene body Promoter (~ 1.5–2 kb of upstream region) Promoter (~ 0.5 kb of upstream H3K27me3: gene body region) Full name AT4G32540 YUCCA1 Locus IDs Table 1 List of YUCgenes, their expression and histone modifications in response to different environmental signals Tao et al (2008), Hornitschek et al (2012), Muller-Moule et al (2016), Liu et al (2016), Chen et al (2016) and Peng et al (2018) Tao et al (2008), Hornitschek et al (2012), Muller-Moule et al (2016), Liu et al (2016), Chen et a (2016) and Peng et al (2018) Liu et al (2016) Tao et al (2008), Hornitschek et al (2012), Muller-Moule et al (2016), Liu et al (2016) and Chen et al (2016) Chen et al (2016) Tao et al (2008), Hornitschek et al (2012) and Muller-Moule et al (2016) Liu et al (2016) Chen et al (2016) Representative publications Plant Growth Regulation 13 involved in the auxin biosynthesis or signaling pathway in response to shade conditions This PIF7 transcription factor may also recruit an unknown HAT enzyme(s) to promote the histone acetylations such as H4K5ac, H3K9ac, and H3K27ac at the target locus, YUC8, resulting in the induction of its expression (Peng et al 2018) YUCs expression is accompanied by the reduction of H3K27me3 levels Previous chromatin immunoprecipitation-chip (ChIPchip) assays which analyzed the wide-genome distribution of H3K27me3 in the cultured Arabidopsis leaf and callus samples unraveled that this histone modification at different auxin-related gene loci such as YUC4, PIN1, and IAA2 is drastically decreased in callus samples when compared with those in leaves (He et al 2012) In an experiment to test the de novo root organogenesis from Arabidopsis leaf explants cultured on B5 medium under dark conditions, Chen et al (2016) found that YUC1 and YUC4 transcript levels were increased in leaf explants at 4, 8, 12 h after culture and this increase is associated with the reduction of H3K27me3 levels at these gene loci From these results, they hypothesized that wounds may produce some certain signals to employ some epigenetic factors causing the decrease of H3K27me3 levels at YUCs and activate these genes In mammalian and plant cells, POLYCOMB GROUP (PcG) protein complexes have been shown to play in the formation, perpetuation, and epigenetic inheritance of the histone modification—H3K27me3 (Lu et al 2011; Derkacheva and Hennig 2014; Khan et al 2015) On the other hand, different JUMONJI DOMAIN-CONTAINING proteins have been identified to function as HDMs in the mammalian and plant cells (Agger et al 2008; Lu et al 2011; Cheng et al 2018) In Arabidopsis, there are 15 putative active JUMONJI domain HDMs (Lu et al 2008, 2011) In a previous study, the JUMONJI DOMAIN-CONTAINING PROTEIN 12 (JMJ12) which is also called as RELATIVE OF EARLY FLOWERING (REF6) was found to specifically demethylate H3K27me3 and H3K27me2 in Arabidopsis (Lu et al 2011) As we described in above section, wounds may increase the YUCs expression mediating the JA signals Indeed, the JA was also shown to increase the transcript levels of YUC8 and YUC9 (Hentrich et al 2013) Beside the YUC1 and YUC4, by the wide-genome analysis, H3K27me3 is also detected at other YUC loci including YUC2, 3, 5, 6, 8, 9, and 10 (Table 1) (https://epigenomics.mcdb.ucla.edu; Karolchik et al 2003; Casper et al 2018) Thus, it is plausible that the H3K27me3 levels may be also reduced at these gene loci in response to a certain signal which induces the YUCs expression Moreover, some recent studies which performed the ChIP-sequencing assays investigated that YUC1, 3, 7, 8, 9, and 11 are target genes of REF6 (Cui et al 2016; 13 Plant Growth Regulation Li et al 2016; Yan et al 2018) From these, we hypothesize that wound-JA or even other environmental signals may trigger the recruiting of an unknown HDM (such as REF6) to these YUCloci to demethylate H3K27me3 and activate these genes expression (Fig. 2) Possible involvement of H2A.Z nucleosome eviction and YUCs expression in response to warm ambient temperature The warm ambient temperature has been evidenced to induce the auxin biosynthesis genes such as YUC8, YUC9, TAA1, and CYP79B2 leading to increasing the endogenous auxin levels (Stavang et al 2009; Franklin et al 2011; Sun et al 2012) Kumar and Wigge (2010) found that the H2A.Z-containing nucleosomes play as the thermosensors in Arabidopsis This study indicated that the high growth-temperature (27 °C) can promote the eviction of H2A.Z-containing nucleosomes resulting in the alterations of corresponded gene expression (Kumar and Wigge 2010) Based on their results, they proposed that the eviction of H2A.Z-containing nucleosomes at a certain genome region may fascinate the binding of transcription activator to this locus and induce the expression of this gene (Kumar and Wigge 2010) A study reported by the same research group also found that the high temperature promotes the loss of H2A.Z at FLOWERING LOCUS T (FT) gene (Kumar et al 2012) This H2A.Z-containing nucleosome eviction facilitates the binding of PIF4 to FT Fig. 2 Hypothetical working model demonstrates the function of HDM(s) in the regulation of YUCs expression in response to environmental signals Wound-JA or other environmental signals may induce the recruiting of an unknown HDM (such as REF6) to these YUCloci to reduce the H3K27me3 levels and activate these genes Plant Growth Regulation Conclusions and future perspectives Fig. 3 Hypothetical working model demonstrates the role of histone variant H2A.Z in the regulation of YUCs expression in response to warm temperature The warm temperature conditions may induce the eviction of H2A.Z-containing nucleosomes from the YUC loci (such as YUC8) to facilitate the binding of PIF4 proteins to and activate the YUCgenes gene to increase its expression (Kumar et al 2012) Several auxin biosynthesis genes such as YUC8, TAA1, and CYP79B2 were also found to be induced by warm temperature conditions and the induction of transcript levels was abolished when PIF4 is absent in pif4 mutant (Franklin et al 2011; Sun et al 2012) In fact, PIF4 was shown to directly target these genes (YUC8, TAA1, and CYP79B2) and the binding levels were increased in response to warm temperature (Franklin et al 2011; Sun et al 2012) Besides, the warm temperature (28 or 29 °C) was shown to induce the PIF4 transcript levels (Sun et al 2012; Ma et al 2016) Recently, Lee and Seo (2017) the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) proteins directly bind to the YUC9 locus and subsequently represses this gene expression in light-grown seedlings This study also reported that these AHLs can recruit the SWI2/SNF2-RELATED (SWR1) complex to elevate the exchange of H2A-nucleosomes with the H2A.Z-containing nucleosomes at this YUC9 locus (Lee and Seo 2017) However, we have not known that whether the H2A.Z levels are changed at these gene loci under warm temperature growth conditions Based on the current studies, we hypothesize that under the warm temperature conditions, the PIF4 expression is increased and this transcription factor subsequently induces the auxin biosynthesis genes such as YUC8, TAA1, and CYP79B2 in cooperating with the eviction of H2A.Z-containing nucleosomes at these gene loci (Fig. 3) As the result, endogenous auxin levels can be increased to redirect the plant growth in response to warm temperature Auxin is an essential hormone in the plant, therefore, understanding of the pathway and the regulation of auxin biosynthesis are very crucial for plant science and agriculture From the current studies, we can conclude that the chromatin modifications such as histone acetylation and methylation play an important role in the regulation of auxin signaling and biosynthesis genes including different YUCs in response to ambient environmental alterations Besides, the histone variant H2A.Z replacement also imply their functions in the regulation of auxin biosynthesis genes and consequently influence the auxin accumulation in the plants Since the DNA methylation is detected at some YUCgene loci (Table 1), this epigenetic mechanism may also involve in the regulation of these genes Despite the importance of DNA methylation in the regulation of gene expression, there is no direct evidence to indicate whether this epigenetic modification influences the expression of YUCgenes in response to environmental changes Future studies are awaited to elucidate this mystery Overall, the future studies can help to evidence our proposed working models (Figs. 2, 3) and provide more detailed functions of different HDMs and H2A.Z-containing nucleosomes in the regulation of YUCs as well as other auxin-related genes in response to the environmental alterations which are extremely affected by the climate change Not only contributing to our understanding of this topic, these results can be also openly considered as the good direction to help us figure out the better ways to improve the crop growth and production in future Acknowledgements We would like to thank Dr Sara D Siegel (The University of Texas Southwestern, Texas, USA) for her careful and critical reading of our manuscript This work was supported by a Grant from Ho Chi Minh City Open University (to Nguyen Hoai Nguyen, 2018) References Agger K, Christensen J, Cloos PAC, Helin K (2008) The emerging functions of histone demethylases Curr Opin Genet Dev 18:159–168 https://doi.org/10.1016/j.gde.2007.12.003 Aloni R, Aloni E, Langhans M, Ullrich CI (2006) Role of auxin in 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different... aims to provide an overview and some hypotheses of the environmental effects on chromatin modifications which can influence the expression of different YUCs resulting in altering the auxin biosynthesis. .. function in? ?auxin biosynthesis and the influences of? ?environmental factors on these genes expression In Planta, the first identified hormone is auxin and indole3-acetic acid (IAA) is one of main natural