Transcription factor interaction with COMPASS-likecomplex regulates histone H3K4 trimethylation forspecific gene expression in plantsZe-Ting Songa, Le Suna, Sun-Jie Lua, Yongke Tianb, Yong Dingb, and Jian-Xiang Liua,1

aState Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of LifeSciences, Fudan University, Shanghai 200433, China; and bCollege of Life Sciences, University of Science and Technology of China, Hefei 230027, China

Edited by Maarten J. Chrispeels, University of California at San Diego, La Jolla, CA, and approved January 28, 2015 (received for review October 15, 2014)

Accumulation of unfolded or misfolded proteins causes endoplas-mic reticulum (ER) stress, which activates a set of ER membrane-associated transcription factors for protein homeostasis regulation.Previous genome-wide chromatin immunoprecipitation analysisshows a strong correlation between histone H3K4 trimethylation(H3K4me3) and active gene expression. However, how the histonemodification complex is specifically and timely recruited to theactive promoters remains unknown. Using ER stress responsivegene expression as a model system, we demonstrate that sequence-specific transcription factors interact with COMPASS-like compo-nents and affect H3K4me3 formation at specific target sites inArabidopsis. Gene profiling analysis reveals that membrane-associ-ated basic leucine zipper (bZIP) transcription factors bZIP28 andbZIP60 regulate most of the ER stress responsive genes. Loss-of-functions of bZIP28 and bZIP60 impair the occupancy of H3K4me3on promoter regions of ER stress responsive genes. Further, in vitropull-down assays and in vivo bimolecular fluorescence complemen-tation (BiFC) experiments show that bZIP28 and bZIP60 interact withAsh2 and WDR5a, both of which are core COMPASS-like compo-nents. Knockdown expression of either Ash2 or WDR5a decreasedthe expression of several ER stress responsive genes. The COMPASS-like complex is known to interact with histone methyltransferaseto facilitate preinitiation complex (PIC) assembly and generateH3K4me3 during transcription elongation. Thus, our data showsthat the ER stress stimulus causes the formation of PIC and deposi-tion of H3K4me3 mark at specific promoters through the interactionbetween transcription factor and COMPASS-like components.

COMPASS-like | ER stress | H3K4 trimethylation | transcription factor |unfolded protein response

Packing of DNA with histone octamer into chromatin providesa sophisticated regulatory module for diverse gene regulation

patterns in response to external environmental or internal de-velopmental cues in eukaryotic cells (1). Posttranslational mod-ifications of histones directly or indirectly regulate chromatinstate, and they therefore are important for gene expression andheterochromatin silencing (2–4). For example, acetylation in theglobular core histone H3 enables recruitment of the SWI/SNFnucleosome remodeling complex to facilitate gene transcriptionin yeast (5, 6). In contrast, histone H3 methylation does not af-fect chromatin structure per se, but interacts with additionalfactors such as the Complex Proteins Associated with Set1/Set1Complex (COMPASS)/SET1C in yeast (7) or COMPASS-likecomplex in mammals (8), which contains three structural corecomponents BRE2/Ash2, SWD3/WDR5, and SWD1/RbBP5,and H3K4 methyltransferases such as Set1 in yeast or MLL1 inmammals (8). Recently, the COMPASS-like complex was alsoreported to be well conserved in Arabidopsis plants (9).Genome-wide chromatin immunoprecipitation analysis reveals

that there is a strong correlation between histoneH3K4 trimethylation(H3K4me3) and active gene expression in yeast (10), mammal (11,12), and plants (13, 14). Despite the controversy on whether histoneH3K4me3 conferred by the Trithorax family proteins promotes

gene transcription, more experiments favor that H3K4me3 mod-ification is the cause of gene transcription (15, 16). Depletion ofhistone H3K4me3 affects the expression of specific genes in yeast,mammals, and plants (9, 17–19), although depletion of H3K4me3has little effect on global gene expression in yeast (18). Furtherstudy in Arabidopsis has demonstrated that the COMPASS-likecomplex not only facilitates transcription preinitiation complex(PIC) assembly, but also generates trimethylated histone at H3K4that is important for gene-specific transcription (20). In humancells, trimethylated histone at H3K4 interacts with TAF3, part ofthe basal transcription factor TFIID, to direct global TFIID re-cruitment to active genes, some of which are p53 targets (21, 22).In vitro studies with recombinant chromatin and purified humanfactors showed a causal role for COMPASS/SET1C-mediatedH3K4me3 in p53-dependent transcription (23). However, howhistone modification complex is specifically and timely recruitedto the promoters to potentiate active gene expression remainsunanswered. We have studied this question by using the stressresponsive gene expression system that is triggered by the ac-cumulation of unfoled or misfolded proteins in the endoplasmicreticulum (ER).Protein folding is fundamentally important for eukaryotic cells.

A collection of conserved signaling pathways, termed the unfoldedprotein response (UPR), monitors protein folding status in theER, and coordinates protein folding capacity with protein folding

Significance

In metazoans, pausing of Pol II during early elongation isa widespread regulatory mechanism for transcription regula-tion. However, preinitiation complex (PIC) assembly is moreimportant for transcription in plants. Chromatin remodelingand histone modifications are considered important for accessof protein factors to the underlying DNA sequences. However,how histone modifications are specifically and timely gener-ated at active promoters is less understood. COMPASS-likecomplex plays a critical role in PIC assembly and histone H3K4trimethylation. We found that Arabidopsis transcription factorsbZIP28/bZIP60 interact with COMPASS-like components both invitro and in vivo. We present a general model on how histoneH3K4 trimethylation is specifically formed during induciblegene expression by using the endoplasmic reticulum (ER) stressresponse system in Arabidopsis plants.

Author contributions: Z.T.S., L.S., and J.X.L. designed research; Z.T.S. and L.S. performedresearch; S.J.L., Y.T., and Y.D. contributed new reagents/analytic tools; Z.T.S. and J.X.L.analyzed data; and J.X.L. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The microarray data reported in the paper have been deposited in theArrayExpress database, www.ebi.ac.uk/arrayexpress (accession no. E-MTAB-2657).1To whom correspondence should be addressed. Email: jianxiangliu@fudan.edu.cn.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1419703112/-/DCSupplemental.

2900–2905 | PNAS | March 3, 2015 | vol. 112 | no. 9 www.pnas.org/cgi/doi/10.1073/pnas.1419703112

Dow

nloa

ded

by g

uest

on

July

9, 2

020

demands according to different developmental programs and en-vironmental conditions (24–26). For gene transcriptional control,two ER-membrane-associated transcription factors, ATF6 andXBP1, play important roles in UPR in animal cells (27). Theseproteins reside on the ER membrane under normal condition.When unfolded or misfolded proteins accumulate in the ER, ATF6is translocated from ER to Golgi apparatus, where it is sequentiallycleaved by S1P and S2P proteases, and the N terminus containingthe DNA binding and transcriptional activation domains enters thenucleus to activate downstream gene expression (28). Activationmechanism of XBP1 is similar to that of Hac1 in yeast in whichIRE1-regulated unconventional splicing results in an ORF shiftand elimination of the transmembrane domain, enabling the nu-clear localization of the newly encoded XBP1 (29, 30). Using themodel plant Arabidopsis, two ER membrane-associated transcriptionfactors, bZIP28 and bZIP60, were identified as the plant counter-parts of mamalian ATF6 and XBP1, which are activated through theregulated intramembrane proteolysis and unconventional splicing inresponse to ER stress, respectively (31–33). In general, when themembrane-associated transcription factors are activated, they recruitgeneral transcription factors (GTFs) and RNA polymerase II(RNAPII) machinery (34) to the promoters of ER stress-responsivegenes during transcription activation. For these protein factors toaccess the promoter DNA, physical barriers formed by chromatinmust be altered through histone modifiers or chromatin remodelingfactors . However, how the histone modification marks are depositedat specific target sites has not yet been answered. We found thatsequence-specific transcription factors interract with COMPASS-likecomponents Ash2 andWDR5a that are important for histone H3K4trimethylation at specific promoters.

Results and DiscussionbZIP28 and bZIP60 Are Master Transcriptional Regulators in PlantUPR. Previously we and other coworkers demonstrated the im-portant roles of bZIP28 and bZIP60 in the plant UPR (31, 32).Beside the formation of bZIP28 homodimer and bZIP60homodimer, bZIP28 could also interact with bZIP60 in the yeasttwo-hybrid assay (35), in vitro pull-down assay (Fig. S1 A and B),and bimolecular fluorescence complementation (BiFC) assay intobacco (Nicotiana benthamiana) (Fig. S1C). Knockouts of bothbZIP28 and bZIP60 in the double mutant zip28zip60 confer hy-persensitivity to ER stress (Fig. S2) (36). In order to knowwhether bZIP28 and bZIP60 are prerequisite to induce UPRdownstream gene expression in Arabidopsis, we compared theER stress-regulated gene expression profiles of the wild-type(wt) and zip28zip60 plants with the Agilent oligo microarray(V4). Of the 4 × 44 K probes represented on the microarray, 333probes representing 286 genes were up-regulated [fold change(FC) ≥ 2, P ≤ 0.05] by ER stress inducer tunicamycin (TM) inthe wt plants (Fig. 1A and Dataset S1). However, only 6 probesrepresenting 10 genes among them were up-regulated (FC ≥ 2,P ≤ 0.05) by ER stress in the zip28zip60 mutant plants (Fig. 1 Aand B), of which the fold changes of two probes/genes in thezip28zip60 plants were greatly reduced to less than 50% of that inthe wt plants (Dataset S1). There were 48 probes representing 46genes that were up-regulated (FC ≥ 2, P ≤ 0.05) by ER stressspecifically in the zip28zip60 plants, many of them are involved iniron uptake and iron metabolism (Fig. 1A and Dataset S1). ERstress also down-regulated (FC ≤ 0.5, P ≤ 0.05) 170 and 218genes in the wt and zip28zip60 plants, respectively (Fig. 1A andDataset S2). Eight ER stress up-regulated genes from the top list(Dataset S1) were selected, and their expression levels werechecked with quantitative RT-PCR (RT-qPCR) to validate themicroarray results. It was found that except At3g54550 andAt3g12430, whose signal intensities on the microarray were rela-tively low in all of the tested samples (Dataset S1), another sixgenes were highly up-regulated by ER stress in the wt, which weregreatly impaired in the zip28zip60 plants (Fig. 1C). These results

Fig. 1. bZIP28 and bZIP60 are required for transcriptional regulation of ERstress responsive genes. (A) Venn diagrams of the numbers of overlappingand nonoverlapping up-regulated or down-regulated genes from the Ara-bidopsis Agilent oligo microarray (V4) after treatment with TM (5 μg/mL, 4 h)in the wt and zip28zip60 plants meeting of the criteria P ≤ 0.05, fold change(FC) ≥ 2 (for up-regulation) or FC ≤ 0.5 (for down-regulation). (B) Heat mapof differentially up-regulated genes in the wt and zip28zip60 plants fromthe microarray experiment. FC is the value in the TM-treated sample (+TM)divided by that in the nontreated sample (−TM). Only those genes with 3 ≤FC ≤ 10 (P ≤ 0.05) in the wt were used for heat map visualization. Eachhorizontal bar represents a single microarray probe. Green indicates a rela-tively low level of up-regulation, whereas red indicates a relatively high levelof up-regulation. (C) RT-qPCR validation of the microarray results. Relativegene expression is the value of plants treated with TM (5 μg/mL, 4 h) dividedby that of nontreated plants, both of which were normalized to the ex-pression of actin. Bars depict SEM (n = 3).

Song et al. PNAS | March 3, 2015 | vol. 112 | no. 9 | 2901

PLANTBIOLO

GY

Dow

nloa

ded

by g

uest

on

July

9, 2

020

demonstrated that bZIP28 and bZIP60 regulate most, if not all, ofthe downstream genes during the adaptive phase of UPR inArabidopsis.

Loss-of-Function Mutations in bZIP28 and bZIP60 Impair Histone H3K4Trimethylation at Promoters of UPR Genes. To better understandwhether bZIP28 and bZIP60 directly bind to promoters of UPRdownstream genes, chromatin immunoprecipitation (ChIP) experi-ments were carried out with commercial anti-MYC antibody byusing transgenic plants overexpressing MYC-bZIP28 and MYC-bZIP60, in which ER stress induces the activation and nuclearlocation of both MYC-bZIP28 and MYC-bZIP60 (31, 37). qPCRwas performed with primers flanking promoter regions of sixgenes as mentioned above (Fig. S3A). It turned out that duringTM-induced ER stress, both MYC-bZIP28 and MYC-bZIP60were enriched at the promoters of BiP3, TIN1, and ERDJ3A;MYC-bZIP28 was specifically enriched at the promoter ofSARA1A, whereas MYC-bZIP60 was specifically enriched at thepromoter of SEC31A (Fig. 2 A and B). ER stress did not inducethe enrichment of either MYC-bZIP28 or MYC-bZIP60 at thepromoters of NSF, or on the coding region and 3′ UTR region ofBiP3 (Fig. 2 A and B). NSF might be the direct target of othertranscription factors downstream of bZIP28/bZIP60 such asNAC103 (36). Taken together, our ChIP-qPCR results demon-strate that both bZIP28 and bZIP60 are able to directly bind tothe promoter of several UPR genes and share some of the directtargets. It is established that histone H3K4 trimethylation at pro-moters and 5′-end regions significantly correlates with active geneexpression (11, 13, 38, 39). By ChIP-qPCR with antibody againsttrimethylated histone at H3K4, we found that ER stress graduallyinduced H3K4me3 deposition at the promoters of UPR down-stream genes (BiP3, SEC31A, NSF, TIN1, ERDJ3A, and SARA1A)in the wt plants (Fig. 2C). We also checked the pattern of mono-methylation, dimethylation, and trimethylation of histone at H3K4in the zip28zip60 double mutant plants as well as in the wt plants.Interestingly, the ER stress-induced H3K4me3 at promoters ofabove-mentioned UPR genes were abolished in the zip28zip60double mutant (Fig. 2D). However, mutations of bZIP28 andbZIP60 did not have much effect on histone H3K4 dimethylation(H3K4me2) but affected ER stress-induced decrease of histoneH3K4 monomethylation (H3K4me1) at promoters of these UPRgenes (Fig. S3 A–C). Thus, gene-specific transcription factorsbZIP28 and bZIP60 are not only important for up-regulation ofUPR gene expression, but also correlated with histone H3K4me3 atpromoters of strongly induced UPR genes.

bZIP28 and bZIP60 Interact with COMPASS-Like Complex. In yeast andmammals, and in plants, histone H3K4 methylation is catalyzed bythe COMPASS or COMPASS-like H3K4 methyltransferase com-plex (7, 9, 40–42). In Arabidopsis, the COMPASS-like complexcontaining Ash2/ASH2R, WDR5a/WDR5, and RbBP5/RBL de-posits trimethylated but not dimethylated or monomethylatedhistone at H3K4 to the target genes to promote gene expressionfor flowering control (9). Because the ER stress-induced histoneH3K4me3 at UPR gene promoters was impaired in the zip28zip60plants, we were interested in the possible interactions between thetranscription factors (bZIP28 and/or bZIP60) and components inCOMPASS-like complex (Ash2, WDR5a, and/or RbBP5). His- orMBP-tagged forms of Ash2, WDR5a, and RbBP5 were purifiedfrom Escherichia coli and tested for the interactions betweenCOMPASS-like components and the available derivates ofbZIP28 or bZIP60 in the in vitro pull-down assays (Fig. 3A). Itwas found that the activated forms of both bZIP28 and bZIP60could pull down Ash2 or WDR5a (Fig. 3B). In contrast, neitherbZIP28 nor bZIP60 pulled down RbBP5 (Fig. 3B). To confirmthese positive interactions obtained from pull-down assays, BiFCexperiments were performed in tobacco leaves. It was found thatboth bZIP28 and bZIP60 were able to physically interact with

Ash2 or WDR5a in tobacco plants (Fig. 3C). In contrast, inter-actions between transcription factor (bZIP28 or bZIP60) andRbBP5 were not observed (Fig. 3C). Further truncation experiment

Fig. 2. Loss-of-function mutations of bZIP28 and bZIP60 impair enrichmentof histone H3K4 trimethylation on ER stress target genes. (A and B) Directbindings of bZIP28 or bZIP60 to the promoters of ER stress responsive genesin ChIP-qPCR assays. (C and D) Enrichment of trimethylated histone at H3K4on ER stress responsive gene. Plants were treated with TM (5 μg/mL) for 6 hin A, B, and D. Fold change is the DNA enrichment normalized to the non-treated wt control sample, both of which were normalized to the level ofactin. Primers at position a (Fig. S3A) were used for SEC31A, NSF, TIN1,ERDJ3A, and SARA1A. Bars depict SEM (n = 3).

2902 | www.pnas.org/cgi/doi/10.1073/pnas.1419703112 Song et al.

Dow

nloa

ded

by g

uest

on

July

9, 2

020

demonstrated that the DNA binding domain of bZIP28 (aminoacids 138–256) was sufficient for its interaction with Ash2 orWDR5a in the BiFC assays (Fig. S4 A and B). The interactionbetween transcription factor and COMPASS-like appears to begeneral, because another ER-stress-related transcription factorNAC103 (36) also interacts with Ash2 and WDR5a in the BiFCexperiment (Fig. S4C).

Knockdown Expression of Either Ash2 or WDR5a Affects theExpression of ER Stress Responsive Genes. Previous research hasshown that the COMPASS-like components play important rolesin regulating flowering gene expression (9). To know whetherthese components also control the expression of ER stress

responsive genes, RT-qPCR was performed with TM-treated ornontreated wt plants and RNAi mutants of Ash2 orWDR5a. It wasfound that knockdown expression of either Ash2 or WDR5a sub-stantially decreased the up-regulation of ER stress responsivegenes such as BiP3, SEC31A, NSF, TIN1, and SARA1A (Fig. 4 Aand B). To investigate whether knockdown expression of Ash2 orWDR5a also affects enrichment of H4K4 trimethylated histone atUPR genes, CHIP-qPCR was performed. It was found that theER stress-induced H3K4me3 was decreased at UPR genes suchas BiP3 in RNAi plants of either Ash2 or WDR5a comparing tothe wt plants (Fig. S5 A and B). The level of H3K4me3 was notmuch affected at other UPR genes such as ERDJ3A, which might

Fig. 3. bZIP28 and bZIP60 interact with COMPASS-like complex. (A) Schematic structure of bZIP28, bZIP60, and their derivates. The transcriptional activationdomain (TAD), DNA-binding domain (DBD), and transmembrane domain (TMD) are shown. (B) In vitro pull-down assays for the interactions betweentranscription factors and COMPASS-like components. Various fusion proteins were purified from E. coli and used for GST pull-down assays. GST protein wasused as a negative control. (C) In vivo BiFC assays for the interactions between transcription factors and COMPASS-like components. Various pairs of constructswere cotransformed into tobacco (N. benthamiana), and the tobacco epidermal cells were observed under laser confocal microscopy. (Scale bars: 50 μm.)

Song et al. PNAS | March 3, 2015 | vol. 112 | no. 9 | 2903

PLANTBIOLO

GY

Dow

nloa

ded

by g

uest

on

July

9, 2

020

be explained by the remained activity of Ash2 or WDR5a in thetransgenic plants (Fig. S6 A–D). Thus, the COMPASS-likecomplex is also important for specific inducible gene expressionduring the ER stress response in plants.

Recruitment of RNAPII to UPR Gene Promoters Is Defective in thezip28zip60 Mutant Plants. In addition to the important roles ofCOMPASS-like in the assembly of basal transcription machinery,COMPASS-like complex also interacts with the phosphorylatedcarboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII)after PIC assembly in Arabidopsis (20). Further analysis demon-strates that both H3K4 methyltransferase ATX1 and COMPASS-like are required for high-level accumulations of RNAPII andH3K4me3 on ATX1/COMPASS-like regulated genes (20). There-fore, we also examined the occupancy of total RNAPII at above-mentioned UPR genes in both the wt and zip28zip60 double mutantplants. ChIP-qPCR results showed that ER stress induced the en-richment of RNAPII at promoters and coding regions of sixaforementioned UPR genes in the wt plants (Fig. 5 A and B).However, such ER stress-induced enrichments of RNAPII werenot observed in the zip28zip60 double mutants (Fig. 5 A and B).

These results showed that sequence-specific transcription factorsare important for total RNAPII recruitment during induciblegene expression.Fig. 4. Knockdown expression of either Ash2 or WDR5a affects the ex-

pression of ER stress responsive genes. (A and B) ER stress-induced ex-pression of downstream genes in the wt and Ash2 or WDR5a RNAi plants.Fold change is the relative gene expression of plants treated with TM(5 μg/mL, 2 h) divided by that of nontreated plants, both of which werenormalized to the expression of housekeeping gene actin. Bars depictSEM (n = 3).

Fig. 5. Loss-of-function mutations of bZIP28 and bZIP60 affect RNAPII oc-cupancy on UPR gene promoters. (A and B) Enrichment of total RNAPII to thepromoters (A) or coding regions (B) of ER stress responsive genes in ChIP-qPCR assays. Fold change is the DNA enrichment normalized to the non-treated (−TM) wt control sample. The wt and zip28zip60mutant plants weretreated with TM (5 μg/mL, 6 h) and anti-Pol II antibody was used to pre-cipitate RNAPII. Primer position refers to Fig. S3A. Bars depict SEM (n = 3).

Fig. 6. A hypothetical model for the involvement of transcription factor inhistone modification. During the preinitiation complex (PIC) assembly fortranscriptional control in plant UPR, both sequence-specific transcriptionfactor (TF) bZIP28 or bZIP60 and general transcription factors (GTFs) arerecruited to the promoters together with the TATA-box binding protein(TBP) and the mediator. Meanwhile, transcription factor bZIP28 or bZIP60interacts with the COMPASS-like components Ash2 or WDR5a to facilitatethe interraction between COMPASS-like and histone trimethytransferases.Such interaction may generate histone H3K4me3 at promoter regions ofUPR genes. ATX1/COMPASS-like also interracts with the CTD of Pol II, andthe level of H3K4me3 affects the rate of Pol II exit for transcription elon-gation. Other chromatin modifiers such as chromatin remodeling factors andhistone acetyltransferases may also play important roles in this process.

2904 | www.pnas.org/cgi/doi/10.1073/pnas.1419703112 Song et al.

Dow

nloa

ded

by g

uest

on

July

9, 2

020

ConclusionsRecently, computational analysis combined with chromatin im-munoprecipitation followed by sequencing (ChIP-Seq) revealedthat transcription factor binding predicts histone modificationsin human cell lines (43), but the role of transcription factor inhistone modifications over specific gene promoters has not beenexperimentally demonstrated. Our data showed that sequence-specific transcription factor regulates gene expression not only byrecognizing specific DNA sequences, but also by facilitatinghistone modifications such as H3K4me3 at specific DNA sitesthrough interaction with the COMPASS-like components Ash2and WDR5a (Fig. 6). Because the COMPASS-like complex isknown to facilitate PIC assembly and generate H3K4me3, thedata presented here provide evidence on understanding the de-position of histone H3K4me3 mark at specific target sites forinducible gene expression in plants. Such regulation is particu-larly important because much of stress-responsive gene expres-sion in metazoans is mediated at the level of transcriptionelongation (44) whereas plants lack components of promoterproximal pausing, and the Arabidopsis ATX1/COMPASS-likeregulated genes lack preaccumulated Pol II at their 5′ ends (20).

Materials and MethodsPlant Materials and Growth Condition. All of the Arabidopsis thaliana seedsused in this study were in the Col background. Plants were grown at 22 °Cunder white light in a long-day (16-h light/8-h darkness) light photoperiod.Details for generation of RNAi plants are in SI Materials and Methods. Forphenotypic analysis, plants were grown on half strength Murashige andSkoog (MS) plates containing 1% sucrose without or with tunicamycin (TM).For gene expression analysis and CHIP-qPCR, plants were first grown on half-strength MS plates containing 1% sucrose. Subsequently, seedlings werepulled out from the solid medium and subjected to treatments in liquid half-strength MS without or with TM.

Gene Expression Analysis and ChIP-qPCR. Details are in SI Materials andMethods. All of the primers used for RT-qPCR and CHIP-qPCR are listed inTable S1.

In Vitro Pull-Down and in Vivo BiFC Assays. Details are in SI Materials andMethods. Primers for various constructs are listed in Table S1.

ACKNOWLEDGMENTS. We thank Dr. Hongxing Yang for heat map visual-ization. This study was supported by National Basic Research Program ofChina 973 Program Grant 2012CB910500 and National Natural ScienceFoundation of China Grants 31171157, 31222008, and 31470353 (to J.X.L.).

1. Bonasio R, Tu S, Reinberg D (2010) Molecular signals of epigenetic states. Science330(6004):612–616.

2. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature403(6765):41–45.

3. Liu C, Lu F, Cui X, Cao X (2010) Histone methylation in higher plants. Annu Rev PlantBiol 61:395–420.

4. Rea S, et al. (2000) Regulation of chromatin structure by site-specific histone H3methyltransferases. Nature 406(6796):593–599.

5. Williams SK, Truong D, Tyler JK (2008) Acetylation in the globular core of histone H3on lysine-56 promotes chromatin disassembly during transcriptional activation. ProcNatl Acad Sci USA 105(26):9000–9005.

6. Xu F, Zhang K, Grunstein M (2005) Acetylation in histone H3 globular domain regu-lates gene expression in yeast. Cell 121(3):375–385.

7. Miller T, et al. (2001) COMPASS: A complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci USA 98(23):12902–12907.

8. Shilatifard A (2008) Molecular implementation and physiological roles for histone H3lysine 4 (H3K4) methylation. Curr Opin Cell Biol 20(3):341–348.

9. Jiang D, Kong NC, Gu X, Li Z, He Y (2011) Arabidopsis COMPASS-like complexes me-diate histone H3 lysine-4 trimethylation to control floral transition and plant de-velopment. PLoS Genet 7(3):e1001330.

10. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histonemethylase by elongating Pol II provides a localized mark and memory of recenttranscriptional activity. Mol Cell 11(3):709–719.

11. Wang P, et al. (2009) Global analysis of H3K4 methylation defines MLL family membertargets and points to a role for MLL1-mediated H3K4 methylation in the regulation oftranscriptional initiation by RNA polymerase II. Mol Cell Biol 29(22):6074–6085.

12. Barski A, et al. (2007) High-resolution profiling of histone methylations in the humangenome. Cell 129(4):823–837.

13. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wideanalysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thali-ana. Genome Biol 10(6):R62.

14. Li X, et al. (2008) High-resolution mapping of epigenetic modifications of the ricegenome uncovers interplay between DNA methylation, histone methylation, andgene expression. Plant Cell 20(2):259–276.

15. Henikoff S, Shilatifard A (2011) Histone modification: Cause or cog? Trends Genet27(10):389–396.

16. Fromm M, Avramova Z (2014) ATX1/AtCOMPASS and the H3K4me3 marks: How dothey activate Arabidopsis genes? Curr Opin Plant Biol 21:75–82.

17. Jiang H, et al. (2011) Role for Dpy-30 in ES cell-fate specification by regulation ofH3K4 methylation within bivalent domains. Cell 144(4):513–525.

18. Shilatifard A (2012) The COMPASS family of histone H3K4 methylases: Mechanisms ofregulation in development and disease pathogenesis. Annu Rev Biochem 81:65–95.

19. Ding Y, Avramova Z, Fromm M (2011) Two distinct roles of ARABIDOPSIS HOMOLOGOF TRITHORAX1 (ATX1) at promoters and within transcribed regions of ATX1-regu-lated genes. Plant Cell 23(1):350–363.

20. Ding Y, et al. (2012) ATX1-generated H3K4me3 is required for efficient elongation oftranscription, not initiation, at ATX1-regulated genes. PLoS Genet 8(12):e1003111.

21. Lauberth SM, et al. (2013) H3K4me3 interactions with TAF3 regulate preinitiationcomplex assembly and selective gene activation. Cell 152(5):1021–1036.

22. Vermeulen M, et al. (2007) Selective anchoring of TFIID to nucleosomes by trime-thylation of histone H3 lysine 4. Cell 131(1):58–69.

23. Tang Z, et al. (2013) SET1 and p300 act synergistically, through coupled histonemodifications, in transcriptional activation by p53. Cell 154(2):297–310.

24. Walter P, Ron D (2011) The unfolded protein response: From stress pathway to ho-meostatic regulation. Science 334(6059):1081–1086.

25. Hetz C (2012) The unfolded protein response: Controlling cell fate decisions under ERstress and beyond. Nat Rev Mol Cell Biol 13(2):89–102.

26. Liu JX, Howell SH (2010) Endoplasmic reticulum protein quality control and its re-lationship to environmental stress responses in plants. Plant Cell 22(9):2930–2942.

27. Ron D, Walter P (2007) Signal integration in the endoplasmic reticulum unfoldedprotein response. Nat Rev Mol Cell Biol 8(7):519–529.

28. Haze K, Yoshida H, Yanagi H, Yura T, Mori K (1999) Mammalian transcription factorATF6 is synthesized as a transmembrane protein and activated by proteolysis in re-sponse to endoplasmic reticulum stress. Mol Biol Cell 10(11):3787–3799.

29. Rüegsegger U, Leber JH, Walter P (2001) Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfoldedprotein response. Cell 107(1):103–114.

30. Calfon M, et al. (2002) IRE1 couples endoplasmic reticulum load to secretory capacityby processing the XBP-1 mRNA. Nature 415(6867):92–96.

31. Liu JX, Srivastava R, Che P, Howell SH (2007) An endoplasmic reticulum stress responsein Arabidopsis is mediated by proteolytic processing and nuclear relocation ofa membrane-associated transcription factor, bZIP28. Plant Cell 19(12):4111–4119.

32. Iwata Y, Koizumi N (2005) An Arabidopsis transcription factor, AtbZIP60, regulatesthe endoplasmic reticulum stress response in a manner unique to plants. Proc NatlAcad Sci USA 102(14):5280–5285.

33. Deng Y, et al. (2011) Heat induces the splicing by IRE1 of a mRNA encoding a tran-scription factor involved in the unfolded protein response in Arabidopsis. Proc NatlAcad Sci USA 108(17):7247–7252.

34. Weake VM, Workman JL (2010) Inducible gene expression: Diverse regulatorymechanisms. Nat Rev Genet 11(6):426–437.

35. Liu JX, Howell SH (2010) bZIP28 and NF-Y transcription factors are activated by ERstress and assemble into a transcriptional complex to regulate stress response genes inArabidopsis. Plant Cell 22(3):782–796.

36. Sun L, et al. (2013) The plant-specific transcription factor gene NAC103 is induced bybZIP60 through a new cis-regulatory element to modulate the unfolded protein re-sponse in Arabidopsis. Plant J 76(2):274–286.

37. Iwata Y, Fedoroff NV, Koizumi N (2008) Arabidopsis bZIP60 is a proteolysis-activatedtranscription factor involved in the endoplasmic reticulum stress response. Plant Cell20(11):3107–3121.

38. Santos-Rosa H, et al. (2002) Active genes are tri-methylated at K4 of histone H3.Nature 419(6905):407–411.

39. Bernstein BE, et al. (2002) Methylation of histone H3 Lys 4 in coding regions of activegenes. Proc Natl Acad Sci USA 99(13):8695–8700.

40. Schneider J, et al. (2005) Molecular regulation of histone H3 trimethylation byCOMPASS and the regulation of gene expression. Mol Cell 19(6):849–856.

41. Dou Y, et al. (2006) Regulation of MLL1 H3K4 methyltransferase activity by its corecomponents. Nat Struct Mol Biol 13(8):713–719.

42. Wysocka J, et al. (2005) WDR5 associates with histone H3 methylated at K4 and isessential for H3 K4 methylation and vertebrate development. Cell 121(6):859–872.

43. Benveniste D, Sonntag HJ, Sanguinetti G, Sproul D (2014) Transcription factor bindingpredicts histone modifications in human cell lines. Proc Natl Acad Sci USA 111(37):13367–13372.

44. Adelman K, Lis JT (2012) Promoter-proximal pausing of RNA polymerase II: Emergingroles in metazoans. Nat Rev Genet 13(10):720–731.

Song et al. PNAS | March 3, 2015 | vol. 112 | no. 9 | 2905

PLANTBIOLO

GY

Dow

nloa

ded

by g

uest

on

July

9, 2

020