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. 2017 Jul 17;18(1):538.
doi: 10.1186/s12864-017-3929-6.

Ethylene Induces Combinatorial Effects of Histone H3 Acetylation in Gene Expression in Arabidopsis

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Free PMC article

Ethylene Induces Combinatorial Effects of Histone H3 Acetylation in Gene Expression in Arabidopsis

Likai Wang et al. BMC Genomics. .
Free PMC article

Abstract

Background: Histone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in ethylene signaling; however, few studies have investigated how ethylene signaling regulates the genomic landscape of chromatin states. Recently, we found that ethylene can specifically elevate histone H3K14 acetylation and the non-canonical histone H3K23 acetylation in etiolated seedlings and the gene activation is positively associated with the elevation of H3K14Ac and H3K23Ac in response to ethylene. To assess the role of H3K9, H3K14, and H3K23 histone modifications in the ethylene response, we examined how ethylene regulates histone acetylation and the transcriptome at global level and in ethylene regulated genes both in wild type (Col-0) and ein2-5 seedlings.

Results: Our results revealed that H3K9Ac, H3K14Ac, and H3K23Ac are preferentially enriched around the transcription start sites and are positively correlated with gene expression levels in Col-0 and ein2-5 seedlings both with and without ethylene treatment. In the absence of ethylene, no combinatorial effect of H3K9Ac, H3K14Ac, and H3K23Ac on gene expression was detected. In the presence of ethylene, however, combined enrichment of the three histone acetylation marks was associated with high gene expression levels, and this ethylene-induced change was EIN2 dependent. In addition, we found that ethylene-regulated genes are expressed at medium or high levels, and a group of ethylene regulated genes are marked by either one of H3K9Ac, H3K14Ac or H3K23Ac. In this group of genes, the levels of H3K9Ac were altered by ethylene, but in the absence of ethylene the levels of H3K9Ac and peak breadths are distinguished in up- and down- regulated genes. In the presence of ethylene, the changes in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expressions.

Conclusions: Our study reveals that the plant hormone ethylene induces combinatorial effects of H3K9Ac, K14Ac and K23Ac histone acetylation in gene expression genome widely. Further, for a group of ethylene regulated genes, in the absence of ethylene the levels and the covered breadths of H3K9Ac are the preexist markers for distinguishing up- and down- regulated genes, the change in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expression in the presence of ethylene.

Keywords: Arabidopsis; Combinatorial effects; Ethylene; Histone acetylation.

Conflict of interest statement

Ethics approval and consent to participate

The seed samples used in this study were publicly available and de-identified, and obtained from the following sources: The Arabidopsis Information Resource (TAIR, https://www.arabidopsis.org).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Histone acetylation marks are enriched around transcription start sites (TSS) and are positively correlated with gene expression levels in Arabidopsis. a Heat maps show H3K9Ac, H3K14Ac, and H3K23Ac enrichment (IgG normalized reads per kilobase (kb) per million mapped reads (RPKM)) at all genes in Arabidopsis along with relative mRNA values. Scatter plot for mRNAs ranked according to gene expression levels in 3-day-old Col-0 seedlings under air treatment. Heat maps are ranked according to gene expression levels. b H3K9Ac, H3K14Ac, and H3K23Ac peak distributions at the TSS and 200 bp downstream of the TSS (TSS + 200 bp), in intragenic regions (inside exons or introns excluding the peaks that overlapped with the TSS + 200 bp and 3′ UTR), in 3′ UTRs, and in intergenic regions (upstream and downstream of genes). c H3K9Ac, H3K14Ac, and H3K23Ac were highly enriched in genes compared to transposable elements (TEs). IgG normalized RPKM in gene body from the TSS to the transcription termination site (TTS) for each histone mark was calculated in all genes and for TEs. d-f Mean enrichment profiles (Log2 RPKM (ChIP/IgG)) along gene bodies of reads for d H3K9Ac, e H3K14Ac, and f H3K23Ac. Genes were ranked according to relative mRNA expression levels and divided into five equal sets
Fig. 2
Fig. 2
Genome-wide analysis of H3K9Ac, H3K14Ac and H3K23Ac in etiolated seedlings in the absence of ethylene. a Overlap of peak-associated genes among H3K9Ac, H3K14Ac and H3K23Ac in Col-0 under air treatment. The nearest gene was assigned to each peak if there was more than one gene within 5 kb. b The correlation of histone enrichment (RPKM) of H3K14Ac vs. H3K23Ac; H3K14Ac vs. H3K9Ac; and H3K23Ac vs. H3K9Ac in gene body regions with transcript abundance in the absence of ethylene. “All genes” indicates the total genes in Arabidopsis. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. c Boxplot showing the association of transcript levels of gene expression and histone acetylation in Col-0 without ethylene treatment. Gene expression level was Log2-transformed. “All genes” indicates the total genes in Arabidopsis; K9 K14 K23, genes marked by H3K9Ac, H3K14Ac and H3K23Ac, n = 2400; K14 K23, genes specifically marked by H3K14Ac and H3K23Ac but not H3K9Ac, n = 172; K14 K9, genes specifically marked by H3K14Ac and H3K9Ac but not H3K23Ac, n = 202; K23 K9, genes specifically labeled by H3K23Ac and H3K9Ac but not H3K14Ac, n = 1529; K14, K23, and K9, peak associated genes uniquely marked by K14 (n = 25), K23 (n = 513), and K9 (n = 5927), respectively; none indicates genes not associated with H3K9Ac, H3K14Ac, or H3K23Ac peaks. The ** indicates P = 5.49 × 10−11 by t-test. d-f Boxplots showing the correlation of peak breadths for H3K9Ac (d), H3K14Ac (e), and H3K23Ac (f) with gene expression levels in genome wide. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. The ** indicates P ≤ 3.25 × 10−18 by t-test. No significant differences within gene groups were detected between H3K14Ac and H3K23Ac gene sets (P value >0.01)
Fig. 3
Fig. 3
Combined enrichment of H3K9Ac, H3K14Ac, and H3K23Ac is correlated with high gene expression levels in the presence of ethylene. a Overlap of genes marked by H3K9Ac, H3K14Ac and H3K23Ac under ethylene treatment. b Boxplot showing the association of transcript levels of gene expression and histone acetylation in Col-0 with ethylene treatment Gene expression levels were Log2-transformed. “All genes” indicates the total genes in Arabidopsis; K9 K14 K23, genes marked by H3K9Ac, H3K14Ac and H3K23Ac, n = 9120; K14 K23, genes marked by H3K14Ac and H3K23Ac but not H3K9Ac, n = 343; K14 K9, genes marked by H3K14Ac and H3K9Ac but not H3K23Ac, n = 1909; K23 K9, genes marked by H3K23Ac and H3K9Ac but not H3K14Ac, n = 1339; K14, K23, and K9, genes uniquely marked by K14 (n = 799), K23 (n = 358), or K9 (n = 3455); none, genes that could not be assigned to peaks of H3K9Ac, H3K14Ac, or H3K23Ac. The ** indicates P < 6.04 × 10−6 by t-test. c Boxplot showing peak breadths under ethylene treatment plotted based on transcript abundance. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. The ** indicates P < 0.001 by t-test. d-f Scatter plots of mean histone enrichment of d H3K9Ac, e H3K14Ac, and f H3K23Ac in ethylene treatment vs. air. To generate the graph, histone reads density were normalized using MAnorm [37] and normalized peak enrichments in ethylene vs. air were plotted for sets of genes clustered based on transcript abundance in air. Solid black lines in the plots denote the linear regression line. g-i Volcano plots for g H3K9Ac, h H3K14Ac, and i H3K23Ac showing the differential enrichment (Rescaled M value versus Rescaled A value after MAnorm normalization [37]) for each individual peak detected in the comparison of plants grown in ethylene vs. air. M = log2 (Read density in C2H4/Read density in air) and A = 0.5 × log2 (Read density in C2H4 × Read density in air). Red dots represent data with P ≤ 0.05 and |M| ≥0.4
Fig. 4
Fig. 4
The ethylene-induced shift of histone acetylation marks is EIN2 dependent. a Heat maps show H3K9Ac, H3K14Ac and H3K23Ac enrichment (IgG normalized reads per kilobase per million mapped reads (RPKM)) in ein2-5 at all genes in the Arabidopsis which along with relative mRNA values. Scatter plot for mRNAs was ranked according to gene expression levels in Col-0 under air treatment. Heat maps were ranked according to their gene expression levels. b-d Scatter plot shows mean histone enrichment of H3K9Ac (b), H3K14Ac (c) and H3K23Ac (d) in air versus ethylene treatment in ein2-5. To generate the graph, histone peaks were normalized by MAnorm [37], and peak-associated genes were ranked according to relative mRNA expression levels and divided into five equal sets. Then the normalized peak enrichments in air and ethylene condition were plotted. Solid black lines in the plots denote the linear regression line
Fig. 5
Fig. 5
Histone acetylation patterns in ethylene-regulated genes. a Overlap of ethylene-regulated genes marked by H3K9Ac, H3K14Ac, and H3K23Ac in Col-0 under air treatment. b Numbers of Arabidopsis genes that are ethylene up-regulated (ERU), ethylene down-regulated (ERD), and not regulated by ethylene (ERN) based on relative mRNA expression levels divided into five equal sets. c Boxplot showing the correlation of peak breadths and ethylene up-regulated genes (U, n-405) or ethylene down-regulated genes (D, n-634) in COL-0 under air and ethylene treatment. The ** indicates P < 0.001 by t-test. d Boxplot showing the histone mark enrichment (RPKM) in 1000 bp around TSSs in ethylene up-regulated genes (U, n-405) and ethylene down-regulated genes (D, n-634) in Col-0 in air and ethylene. The ** indicates P < 0.001 by t-test
Fig. 6
Fig. 6
Histone acetylation in ethylene regulated genes in ein2-5. a Boxplot showing the peak breadths at their associated- ethylene regulated genes in ein2-5 under air and ethylene treatment. “U” indicates peak associated-ethylene up regulated genes, n = 405; “D” indicates peak associated-ethylene down regulated genes, n = 634. The ** indicates P < 0.001 by t-test. b Boxplot showing the histone marks enrichment (RPKM) in 1000 bp around TSS at their associated- ethylene regulated genes in ein2-5. “U” indicates peak associated-ethylene up regulated genes, n = 405; “D” indicates peak associated-ethylene down regulated genes, n = 634. The ** indicates P < 0.001 by t-test. c-e Heat maps showing c H3K9Ac, d H3K14Ac, and e H3K23Ac differential enrichment (cutoff P ≤ 0.05) on genes differentially expressed in response to ethylene in Col-0 and ein2-5 mutant seedlings. Only the genes marked by H3K9Ac, H3K14Ac, and H3K23Ac in Col-0 plants were used for this heat map. Each line in the heat map represents the representative histone-marked genes, first two lanes of the heat maps in c-e are the normalized M value (obtained using MAnorm, M = log2 (Read density in C2H4/Read density in air)) for differential peaks, and the last lanes of the heat maps in c-e are the fold changes of gene expression

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