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First published online June 11, 2008; 10.1104/pp.108.122929 Plant Physiology 147:2070-2083 (2008) © 2008 American Society of Plant Biologists OPEN ACCESS ARTICLE
Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions1,[W],[OA]Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China (L.G., X.W.D.); National Institute of Biological Science, Zhongguancun Life Science Park, Beijing 102206, China (L.G., J.Z., X.W.D.); and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 (A.A.E., J.-B.F.C., X.W.D.)
Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.
Light is the single most important environmental parameter for plant development. Arabidopsis (Arabidopsis thaliana) can detect all facets of light, such as direction, duration, quantity, and wavelength, and adapt its development to changes in different light parameters (Fankhauser and Chory, 1997  ; Whitelam et al., 1998; Thomas, 2006). Previous work revealed that light causes a large-scale reorganization of chromatin during the floral transition in Arabidopsis (Tessadori et al., 2007) and that the presence or absence of light results in distinct gene expression profiles during the development of Arabidopsis seedlings (Ma et al., 2001; Jiao et al., 2005). The transition of growth from skotomorphogenesis to photomorphogenesis is one example of a light-regulated developmental process in Arabidopsis. Although many protein factors involved in light signaling pathways have been identified by genetic screens (Somers et al., 1991; Wei et al., 1994; Devlin et al., 1998), the detailed mechanisms of light-regulated gene transcription remain obscure. The discovery of light-regulated transcription factors (such as HY5, HYH, and PIF3) and their binding sites (light-responsive cis-elements) provided the first clues about its molecular mechanisms (Chattopadhyay et al., 1998; Ni et al., 1998; Holm et al., 2002). In the dark, pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED/FUSCA (COP/DET/FUS) proteins work cooperatively to inhibit light-induced plant development by ubiquitin-proteasome-mediated degradation of photomorphogenesis-promoting proteins, including transcription factors (Chory and Peto, 1990; Deng et al., 1991; Osterlund et al., 2000; Saijo et al., 2003; Jiao et al. 2007). Collectively, these data suggest the involvement of transcription factors in regulating light-responsive gene transcription and plant development.
Eukaryotic chromatin has a unique structure. Its basic units are nucleosomes, which consist of a histone core around which the DNA helix is wrapped. In this assembly state, the DNA is very compact and the histone proteins block gene expression by hampering the association of transcription factors with their binding sites and preventing the transcription machinery from moving along the DNA strands. A diverse array of posttranslational covalent modifications (e.g. methylation, acetylation, and phosphorylation) of the histone "tails" as well as some histone globular domains can influence nucleosome compaction and access to the DNA (Lee et al., 1993
While the effects of temperature on changes in histone modifications in plants are well known (Sung and Amasino, 2004 In this study, we found that four select histone modifications and the expression levels of representative genes were cooperatively regulated by light. Furthermore, our detailed analysis of changes in the acetylation of H3K9 in seedlings grown under different light conditions suggests that light-regulated changes of histone modifications may be an important component of light-controlled gene transcription during seedling development in Arabidopsis.
Seedlings Grown in Continuous White Light or Darkness Show Different Histone Modification Levels in Representative Light-Regulated Genes
Previous studies (Ma et al., 2001
In order to examine whether light influences histone modifications and whether these light-induced alterations affect gene expression, we performed chromatin immunoprecipitation (ChIP) assays to determine the relative enrichment of four well-studied histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) at these six representative light-regulated loci. Previous studies showed that H3K4me3 is mainly localized in the coding sequence of active genes (Millar and Grunstein, 2006 ; Barski et al., 2007; Li et al., 2007), that H3K9ac tends to have a peak at the promoter region of active genes and extends to the whole coding region (Millar and Grunstein, 2006), and that H3K9me2 and H3K27me3 mostly accumulate in the promoter regions of silent genes (Bastow et al., 2004; Barski et al., 2007; Li et al., 2007). Therefore, we designed the primers for ChIP-qPCR accordingly and selected an amplicon region for H3K4me3 primers at the target genes' 5' coding regions (immediately downstream of the start codon); for H3K9ac, H3K9me2, and H3K27me3-related primers, the amplicon regions were mostly in the promoter regions (Supplemental Table S2). Chromatin fragments were isolated from 6-d-old Columbia-0 (Col-0) wild-type seedlings grown in the dark or in continuous white light. After incubating with specific antibodies against H3K4me3, H3K9ac, H3K9me2, and H3K27me3 individually, the precipitated DNA was analyzed by qPCR (Table II
). The enrichment of ChIP fragments relative to nonprecipitated (input) DNA was calculated according to Frank et al. (2001). We found that the histone modifications studied differed for most genes when white light and dark growing conditions were compared. When comparing RT-qPCR data (Table I) with ChIP-qPCR data (Table II), we found that five genes showed an increase in H3K4me3 or H3K9ac under white light or darkness in parallel to increased transcript levels in the same light environment. In contrast, H3K9me2 and H3K27me3 were enriched in darkness for four genes, while the transcript levels of the respective genes were up-regulated in white light. This means that changes in histone modifications and gene transcript levels are cooperatively regulated by light during Arabidopsis development. Interestingly, the degree of alterations of histone modifications was less pronounced than the gene expression level changes. This suggests that relatively small alterations in histone modifications might cause large changes in gene expression.
H3K9ac Correlates with mRNA Levels and Is Set Up in a Developmentally Dependent Manner Based on our RT-qPCR and ChIP-qPCR data detailed above, we selected four representative genes for which we found strong indications for a correlation of histone modifications and transcript levels. Here, we examined a possible light-regulated relationship between H3K9ac enrichment and mRNA steady-state levels in detail by conducting a time course experiment in which wild-type seedlings (Col-0) were grown in continuous darkness for 6 d and then moved to white light for 0, 2, 4, 6, or 24 h. If a correlation exists between histone modifications and light-regulated gene expression, alterations in modification status and gene expression should follow similar patterns. RT-qPCR data shown in Figure 1A demonstrate that two of the genes, PSII light-harvesting complex gene 1.4 (At2g34430) and ribulose bisphosphate carboxylase small chain 1B (At5g38430), were light up-regulated, while the other two, peroxidase 21 (At2g37130) and citrate synthase 3 (At2g42790), were light down-regulated. Furthermore, we performed ChIP assays followed by qPCR to determine the enrichment of H3K9ac using the same biological material as for the RT-qPCRs to determine the mRNA levels. We found that for genes that were up-regulated by light, the relative abundance of H3K9ac also increased with extending exposure to white light. For PSII light-harvesting complex gene 1.4 (At2g34430), the correlation coefficient between ChIP-qPCR and RT-qPCR data was 0.97; for ribulose bisphosphate carboxylase small chain 1B (At5g38430), the correlation coefficient was 0.85. This means that gene transcription and H3K9ac are highly correlated for these two genes. Conversely, relative H3K9ac enrichment decreased in light-down-regulated peroxidase 21 (At2g31730) the longer the plants were exposed to white light, although the expression level was up-regulated 2 h after the seedlings were transferred to light (Fig. 1B). At later time points, histone modifications were correlated with the gene expression. H3K9ac of citrate synthase 3 (At2g42790) did not show a dramatic down-regulation; however, its overall pattern corresponded well to our RT-qPCR data for this gene, especially after 2 h of light exposure. These results suggest that H3K9ac is regulated by light and that the mRNA levels of the four representative genes chosen here might be correlated with the relative enrichment of H3K9ac.
At comparative time points, H3K9ac and gene expression changes did not show obvious alterations compared with dark-grown seedlings transferred to light (Fig. 1). We also conducted experiments in which white light-grown seedlings were transferred to darkness (data not shown). This result suggests that effects due to the decline of light signals are much slower than those due to light activation. To investigate when during seedling development the observed H3K9ac patterns are set up for all four genes and whether these patterns are stable, we examined the relative enrichment of H3K9ac in 3-, 6-, and 9-d-old Col-0 wild-type seedlings grown in continuous white light or darkness with ChIP-qPCR experiments. We found that H3K9ac was set up already at the earliest time point studied for both light-up-regulated genes: PSII light-harvesting complex gene 1.4 (At2g34430) and ribulose bisphosphate carboxylase small chain 1B (At5g38430; Fig. 2 ). While the histone acetylation level remained stable for At5g38430, it fell slightly for At2g34430 once the seedlings were 6 d old. Interestingly, the H3K9ac enrichment took longer in the light-down-regulated than in the light-up-regulated genes. For both peroxidase 21 (At2g37130) and citrate synthase 3 (At2g42790), the levels of H3K9ac were almost identical for seedlings grown in white light or darkness after 3 d and showed significantly higher levels only at the 6- and 9-d time points (Fig. 2). These data indicate that light-controlled H3K9ac patterns are set up within the first week of seedling development, but at different time points and in a gene-specific manner depending on whether the respective genes are up- or down-regulated by light.
H3K9ac Enrichment Is Affected by Light Intensity and Light Wavelength
Previous studies (Ma et al., 2003
Second, we determined the effects of different light wavelengths on the relative enrichment of H3K9ac. We found that H3K9ac was up-regulated in PSII light-harvesting complex gene 1.4 (At2g34430) and ribulose bisphosphate carboxylase small chain 1B (At5g38340) when Col-0 wild-type seedlings were grown in continuous color lights, as in white light. In general, seedlings did not show significant differences in H3K9ac in light-down-regulated peroxidase 21 (At2g37130) and citrate synthase 3 (At2g42790) when continuously exposed to different light wavelengths. The only exception to this was a pronounced decline in H3K9ac in At2g37130 when seedlings were grown in blue light (Fig. 4A ). Collectively, these results suggest that H3K9ac responds gene specifically to changes in the light spectrum.
H3K9ac in phy and cry Photoreceptor Mutants Depends on Light Wavelength To dissect the relationship between H3K9ac and light color in more detail, we examined H3K9ac enrichment in 6-d-old wild-type seedlings and photoreceptor mutants that were continuously exposed to different light wavelengths (or darkness) during their growth. We found that for the light-up-regulated PSII light-harvesting complex gene 1.4 (At2g34430) and ribulose bisphosphate carboxylase small chain 1B (At5g38430), the H3K9ac enrichment levels were higher in wild-type seedlings compared with phyB phyD phyE, cry1 cry2, and phyA phyB phyE photoreceptor mutants in all three light colors studied (red, blue, and far red). Genes that were down-regulated by light, peroxidase 21 (At2g37130) and citrate synthase 3 (At2g42790), showed the opposite (i.e. wild-type seedlings had a lower level of H3K9ac for these genes than mutant lines grown in the same light conditions, with the exception of far red light in At2g37130; Fig. 4B). The phyB phyD phyE, phyA phyB phyE, and cry1 cry2 mutants used here are in different genetic backgrounds (Landsberg erecta [Ler] and Col, respectively, as detailed in "Materials and Methods"). However, an analysis of H3K9ac enrichment and mRNA levels for the genes under study in various Arabidopsis ecotypes showed that all genetic backgrounds behaved in a very similar fashion (Supplemental Fig. S1). Therefore, it can be reasonably assumed that the differences in H3K9ac enrichment observed here are based on the differences in light color and are gene specific rather than based on the genetic background of the wild-type and mutant plants used.
To investigate the relationships between H3K9ac and gene expression in detail, we analyzed an Arabidopsis line with a T-DNA insertion in the HD1 gene (Supplemental Fig. S2). HD1 is one of 18 known HDACs in Arabidopsis (Pandey et al., 2002
Furthermore, we determined the transcription level of these representative genes. Standard controls routinely used in RT-qPCR assays to analyze the mRNA steady-state level of genes, such as actin and tubulin, cannot be chosen for HDAC mutant lines because the acetylation level of such control genes is affected by hd1 mutations as well. This means that the transcript levels of these standard control genes do not remain constant in HDAC mutant lines, which prevents reliable quantification of the target genes. Previous reports circumvented this problem by using rRNA as normalization and loading equal amounts of total rRNA in RNA gel-blot assays instead (Benhamed et al., 2006 ). For RT-qPCR approaches, however, this issue remains an obstacle. Since the net transcript accumulation in RNA gel-blot assays depends on the rate of transcription and the kinetics of degradation (Folta and Kaufman, 2006), we took the binding capability of RNA polymerase II (Pol II) as a more direct index to determine the transcript level of the representative genes under study in our hd1 mutant analysis. In other species (e.g. human), this index has been used successfully (Barski et al., 2007; Garcia-Bassets et al., 2007). We performed a ChIP assay with an antibody against Arabidopsis Pol II and then analyzed the relative enrichment of the genes under study in Pol II ChIP samples relative to input samples using qPCR (see Supplemental Table S4 for primers). We found that the transcript levels of all four genes under study were significantly higher in hd1 mutants compared with wild-type plants in light- and dark-grown seedlings (Fig. 5B). The Pol II ChIP-qPCR results were very similar to our findings for H3K9ac (Fig. 5A) in that a higher relative enrichment for H3K9ac and Pol II binding was observed in hd1 mutants. This means that a correlation between HD1-regulated H3K9ac levels and Pol II binding capabilities exists at the loci surveyed here. Furthermore, our data suggest that HD1-involved H3K9ac regulation of gene expression might function through an alteration of Pol II binding capacity.
As one of the key factors in the photomorphogenesis pathway, DET1 has been shown to regulate gene expression in response to light signals through protein degradation (Yanagawa et al., 2004
H3K9ac Is Suppressed in hy5 Mutants
HY5 is a well-known transcription factor that can mediate light-induced gene expression (Chattopadhyay et al., 1998
Moreover, we analyzed the mRNA steady-state levels of the four representative genes under study in hy5-215 mutant and wild-type lines and found a significant reduction in the transcripts of light-up-regulated genes in a hy5-215 mutant background in white light-grown plants (Fig. 7B). Little difference was found at light-down-regulated loci in dark-grown samples, which is consistent with our results for H3K9ac and previous reports that HY5 promotes photomorphogenesis but is only responsible for limited contributions in the dark due to degradation (Ang et al., 1998 ; Chattopadhyay et al., 1998).
Distinct histone modifications are not distributed equally over the entire gene territory but have specific spatial patterns that are tightly regulated and essential for their effects on transcription (Millar and Grunstein, 2006
Second, we surveyed the spatial distributions of H3K9ac and Pol II in different regions of At2g34420 and At2g34430 in both 6-d-old hy5-215 mutant and wild-type seedlings using 15 primer pairs (Supplemental Table S5). The primers used here spanned the entire territories of these two genes, including their putative promoter region (Fig. 8A). The amplified products were sequenced to confirm the specificity of the primers. We found that H3K9ac was enriched in the coding region of both genes as well as their promoter in seedlings grown in white light. The relative abundance of H3K9ac was lower in dark-grown seedlings compared with those grown in white light and showed a relatively uniform spatial distribution. H3K9ac enrichment in white light-grown hy5-215 mutants decreased throughout the entire gene territory relative to wild-type seedlings (Fig. 8B). However, no significant differences could be detected between hy5 and wild-type lines cultivated in the dark. Third, we observed that Pol II accumulated in the coding regions of both genes under study, but not in the promoter region (Fig. 8C). Furthermore, similar to our findings for H3K9ac, the level of Pol II was higher in white light-grown wild-type seedlings than in hy5 mutants, while no differences could be detected in dark-grown plants. Results obtained from RT-qPCR confirmed the Pol II-ChIP data and showed that the steady-state mRNA levels of At2g34420 and At2g34430 were reduced in hy5 mutants grown in white light (data not shown). Together, these results suggest that light-dependent HY5-induced transcription is influenced by H3K9ac in light-regulated genes.
It has been reported that different histone modifications have individual distribution patterns, which might hint at specific functions during gene transcription (Li et al., 2007
Using a ChIP-qPCR approach, we showed that light cooperatively regulates histone modifications and transcript levels of representative genes during seedling development in Arabidopsis. Collectively, our data suggest that changes in histone modifications might be a key process in plant responses to different light environments.
Our experiments delivered multiple lines of evidence to support a model in which histone modifications are influenced by light during Arabidopsis seedling development. First, we found that the enrichment of select histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) showed marked differences at representative loci in the presence or absence of light (Table II). Second, transferring dark-grown 6-d-old seedlings into white light was accompanied by changes in H3K9ac patterns (Fig. 1B). Third, we demonstrated that H3K9ac was affected by changes in light intensity and wavelength (Figs. 3B and 4), which could mean that different photoreceptors are involved in altering histone modifications. For this study, only partial photoreceptor mutants were available, such that not the entire light signaling pathway was blocked. The diversity and functional redundancy of photoreceptors might explain why the levels of H3K9ac in mutants were higher than in dark-grown wild-type seedlings. Previous studies suggested that PHYA is the primary photoreceptor for the far-red signaling pathway (Wang et al., 2002
Studies from yeast and mammalian cells showed that different histone modifications have different correlations with gene expression (Jenuwein and Allis, 2001
In our work, we also noticed that not all histone modification signals were correlated with gene expression. Previous studies in other organisms have observed roles for alterations in histone modifications in almost all DNA-related metabolic processes (Jenuwein and Allis, 2001
Previous studies showed that H3K9me2 and H3K27me3 act as gene repressors by binding to promoter regions (Barski et al., 2007
In this study, we specifically analyzed the possibility of H3K9ac being a transcription regulator during light-controlled plant development. A potential connection between histone acetylation and light-activated transcription has been proposed before (Chua et al., 2001
In mammals, gene transcription has been described as a cascade of recruitment events involving various coactivator complexes: transcription factors bind to cis-elements, which are located in an approximately 200-bp nucleosome-free region at the SST region of active genes. At the same time, they can interact with transcriptional cofactors. The resulting complexes have been shown to induce histone acetylation, chromatin remodeling, and other structural chromatin changes. Subsequently, RNA polymerase initiation complexes are recruited to start transcription (Agalioti et al., 2000
Earlier genetic and biochemical studies have indicated that components of the photomorphogenesis pathway, such as COP10, DDB1a, and DET1, can form a so-called CDD complex (Yanagawa et al., 2004
Plant Material and Growth Conditions
The wild-type genotype used in this work was Arabidopsis (Arabidopsis thaliana) ecotype Col-0 unless specified otherwise. Furthermore, we used the following mutants: cry1-304 cry2-1 (Col-0 background; Mockler et al., 1999
ChIP was performed as described before (Gendrel et al., 2005 ChIP DNA was analyzed by qPCR (ABI 7500; ABI), in which TaKaRa SYBR Premix ExTaq was used as the reaction system. Specific primers (Supplemental Tables S1–S5) were designed, and the PCR products were sequenced to validate that only the desired target region was amplified.
Quantification of immunoprecipitated DNA was performed as described (Frank et al., 2001
Total RNA was extracted with TRIzol (Invitrogen) from the same seedling samples that were used for the ChIP assay. After DNase I (Promega) digestion, RNA was reverse transcribed with SuperScript II reverse transcriptase (Invitrogen). cDNA was analyzed by relative qPCR. Specific primers (Supplemental Table S1) were designed, and the PCR products were sequenced to validate that only the desired target region was amplified. Actin (At5g09810) was used as an endogenous control to normalize the relative expression level. cDNA from 6-d-old dark-grown Col-0 wild-type seedlings was used for normalization and defined as 1. The data were analyzed with ABI 7500 System SDS software (version 1.2.3). At least three independently performed experiments on independent tissue samples were analyzed.
The following materials are available in the online version of this article.
We thank Dr. Ligeng Ma for providing homozygous hd1 mutants. We thank Ligeng Ma, Jian Li, Hang He, and Feng Wang for helpful discussions and Fangwen Fu for critical reading of the manuscript. Received May 14, 2008; accepted June 3, 2008; published June 11, 2008.
1 This work was supported by the National "863" High-Tech Project of the National Ministry of Science and Technology (grant no. 2003AA 210070), People's Republic of China, and by the National Institutes of Health (grant no. GM–47850 to X.W.D.).  The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Xing Wang Deng (xingwang.deng{at}yale.edu).
[W] The online version of this article contains Web-only data.
[OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.108.122929 * Corresponding author; e-mail xingwang.deng{at}yale.edu.
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