A novel bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis
- Carnegie Institution for Science, Department of Plant Biology, United States
- Department of Bioengineering, Stanford University, United States
- Chan Zuckerberg Biohub, United States
Figures
Figure 1 with 2 supplements
Patterns of epigenetic modification across metabolism in Arabidopsis.
(A) Enrichment analysis shows different epigenetic modification patterns across metabolic domains. The heatmap represents log2 fold change (Log2FC) of enrichment or depletion of an epigenetic mark …
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Figure 1—source data 1
Source data used to generate Figure 1A, B.
- https://cdn.elifesciences.org/articles/69508/elife-69508-fig1-data1-v2.xlsx
Figure 1—figure supplement 1
Correlation analysis of epigenetic marks based on their relative abundance on (A) total Arabidopsis metabolic genes, (B) non-specialized metabolic genes.
Epigenetic modifications are color-coded based on their effect on gene expression; red represents activating mark and blue represents repressing mark. r represents Pearson’s correlation coefficient. …
Figure 1—figure supplement 2
Epigenetic marks associated with pathways involved in specialized metabolism including camalexin biosynthesis.
The heatmap represents log2 fold change (Log2FC) of enrichment or depletion of a mark associated with each pathway relative to total metabolic genes based on Fisher’s exact test followed by a post …
Figure 2
H3K27me3 and H3K18ac are co-localized on camalexin biosynthesis genes in planta to form a bivalent chromatin.
(A) Camalexin biosynthesis pathway map and the essential genes that can produce camalexin. (B-C) Sequential chromatin immunoprecipitation (ChIP)-qPCR confirms the co-localization of H3K27me3 and …
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Figure 2—source data 1
Source data used to generate Figure 2B,C.
- https://cdn.elifesciences.org/articles/69508/elife-69508-fig2-data1-v2.xlsx
Figure 3 with 4 supplements
H3K27me3-H3K18ac bivalent chromatin controls the timing of gene induction and camalexin accumulation upon a pathogen signal.
(A-C) Expression of the three essential genes in camalexin biosynthesis in response to flagellin 22 (FLG22) in the wild type (Col-0), H3K27me3-defective mutants clf28 and pkl-1, and …
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Figure 3—source data 1
Source data used to generate Figure 3A-F.
- https://cdn.elifesciences.org/articles/69508/elife-69508-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
Expression of CYP79B2 in the wild type and mutants in response to flagellin 22 (FLG22).
Significance was tested via two-way ANOVA followed by post hoc Dunnett’s test (*p < 0.05, **p < 0.01, ***p < 0.0001) relative to mock-treated plants at each time point. Results represent the mean of …
Figure 3—figure supplement 2
Expression of CYP71A13 in the wild type and mutants in response to flagellin 22 (FLG22).
Significance was tested via two-way ANOVA followed by post hoc Dunnett’s test (*p < 0.05, **p < 0.01, ***p < 0.0001) relative to mock-treated plants at each time point. Results represent the mean of …
Figure 3—figure supplement 3
Expression of PHYTOALEXIN DEFICIENT 3 (PAD3) in the wild type and mutants in response to flagellin 22 (FLG22).
Significance was tested via two-way ANOVA followed by post hoc Dunnett’s test (*p < 0.05, **p < 0.01, ***p < 0.0001) relative to mock-treated plants at each time point. Results represent the mean of …
Figure 3—figure supplement 4
Camalexin accumulation in the wild type and mutants in response to flagellin 22 (FLG22).
Significance was tested via two-way ANOVA by post hoc Dunnett’s test (*p < 0.05, **p < 0.01, ***p < 0.0001) relative to mock-treated plants at each time point. Results represent the mean of two …
Author response image 1
Additional files
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Supplementary file 1
Log2 fold change in the enrichment analysis to identify specialized metabolic pathways associated with both trimethylation of lysine 27 of histone 3 (H3K27me3) and H3K18ac.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp1-v2.xlsx
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Supplementary file 2
Primers used to quantify the abundance of trimethylation of lysine 27 of histone 3 (H3K27me3) and H3K18ac in the genomic regions of camalexin biosynthesis genes using chromatin immunoprecipitation (ChIP)-qPCR in wild-type and mutant plants with or without flagellin 22 (FLG22) treatment.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp2-v2.docx
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Supplementary file 3
Primers used in the sequential chromatin immunoprecipitation (ChIP)-qPCR experiment to examine the co-localization of trimethylation of lysine 27 of histone 3 (H3K27me3) and H3K18ac within camalexin biosynthesis genes.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp3-v2.docx
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Supplementary file 4
Primers used to examine the expression of camalexin biosynthesis genes under flagellin 22 (FLG22) induction using qPCR.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp4-v2.docx
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Supplementary file 5
The effect of genotype, flagellin 22 (FLG22) treatment, and time point on the expression change of camalexin genes.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp5-v2.docx
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Supplementary file 6
The effect of genotype, flagellin 22 (FLG22) treatment, and time on camalexin accumulation.
- https://cdn.elifesciences.org/articles/69508/elife-69508-supp6-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/69508/elife-69508-transrepform1-v2.docx
