Histone variants shape chromatin states in Arabidopsis
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Austria
- Vienna BioCenter, Austria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Japan
- PRESTO, Japan Science and Technology Agency, Honcho, Japan
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3, Austria
Figures
Figure 1 with 1 supplement
Biochemical analysis of the association between histone variants and histone marks.
(A) Histones H3.1 and H3.3 form homotypic and heterotypic nucleosomes. Spectral counts of H3.1- and H3.3-specific peptides in the respective immunoprecipitations (T – transgenic, E – endogenous H3.1 …
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Figure 1—source data 1
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig1-data1-v1.zip
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Figure 1—source data 2
The data contains the orginal images of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig1-data2-v1.zip
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Figure 1—source data 3
The data contains the orginal images of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig1-data3-v1.zip
Figure 1—figure supplement 1
Biochemical analysis of the association between histone variants and histone marks.
(A) Analysis of DNA in input samples used for H3.1 and H3.3 mononucleosome immunoprecipitation after MNase digestion. (B) Silver-stained 8–20% gradient gel of immunoprecipitated H3.1 and H3.3 …
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Figure 1—figure supplement 1—source data 1
The data contains the orginal images of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig1-figsupp1-data1-v1.zip
Figure 2 with 2 supplements
Histone variants define chromatin states in Arabidopsis thaliana.
(A) Bubble plot showing the emission probabilities for histone modifications/variants across the 26 chromatin states. (The size of the bubble represents the emission probability ranging from 0 to …
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Figure 2—source data 1
This source data contain the original pictures of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
Validation of H2A.2 and H2A.
Z.11 polyclonal antibodies. (A) Sequence alignments of three H2A.Z and four H2A histone variants. Positions that differ between variants are highlighted in blue. Underlined are sequences of peptides …
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Figure 2—figure supplement 1—source data 1
This source data contain the original pictures of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig2-figsupp1-data1-v1.zip
Figure 2—figure supplement 2
Properties of chromatin states in Arabidopsis thaliana.
(A) Heatmap showing the correlation (0–1) between emission parameters of each model. The y-axis represents the distinct states in the reference state model (n=50). The x-axis represents models …
Figure 3 with 2 supplements
Decreased in DNA Methylation (DDM1) loss of function disrupts chromatin states in Arabidopsis thaliana.
(A) Heatmap showing the emission probability for each mark/variant across the 16 chromatin states of the concatenated wild-type and ddm1 mutant model. The bar plot on the left represents the …
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Figure 3—source data 1
The data contains the orginal images of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig3-data1-v1.zip
Figure 3—figure supplement 1
Decreased in DNA Methylation (DDM1) loss of function disrupts chromatin states in Arabidopsis thaliana.
(A) Heatmap showing the emission probability of histone mark/variant across the 15 chromatin states of the concatenated model computed with chromatin profiles from seedlings and leaves. The bar plot …
Figure 3—figure supplement 2
Interaction of Decreased in DNA Methylation (DDM1) and DDM1 deletion mutants with histone variants.
(A–C) Identification of H2A.W and H2A.Z binding sites in DDM1. His6- (A) or GST- (B and C) tagged DDM1 fragments, as indicated with amino acids numbers, were incubated with indicated H2A-H2B dimers …
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Figure 3—figure supplement 2—source data 1
The souce data file contain the original pcitures of the gels.
- https://cdn.elifesciences.org/articles/87714/elife-87714-fig3-figsupp2-data1-v1.zip
Figure 4 with 2 supplements
Impact of expression on chromatin states over TE genes in ddm1.
(A) Enrichment profiles of H2A.W.6 and H2A.Z.9 over TE genes in ddm1. TE genes were grouped by expression in ddm1 mutant. Out of the 3901 TE genes in the Arabidopsis genome annotation, 497 were …
Figure 4—figure supplement 1
Analyses of the parameters that could correlate with the chromatin states with TE expression in ddm1.
Enrichment profiles of histone variants (A) and H3 modifications (B) plotted over groups of TE genes based on their expression in decreased in DNA methylation (ddm1) as defined in the legend for Figu…
Figure 4—figure supplement 2
Analyses of the parameters that could correlate with the chromatin states with TE expression in decreased in DNA Methylation (ddm1).
(A) Box plot showing the expression of the TE genes grouped by the state overlapping the TSS in ddm1. See also Figure 4C. (B) Box plot showing the TE gene length distributions across the five …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | anti-H2A.X.3/5 (Rabbit polyclonal) | Yelagandula et al., 2014 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP | |
| Antibody | anti-H2A.13 (Rabbit polyclonal) | Yelagandula et al., 2014 | WB: 1 μg/ml 5 μg per ChIP | |
| Antibody | anti-H2A.2 (Rabbit polyclonal) | This work (See Materials and methods) | WB: 1 μg/ml 5 μg per ChIP | |
| Antibody | anti-H2A.Z.9 (Rabbit polyclonal) | Yelagandula et al., 2014 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP | |
| Antibody | anti-H2A.Z.11 (Rabbit polyclonal) | This work (See Materials and methods) | WB: 1 μg/ml 5 μg per ChIP | |
| Antibody | anti-H2A.W.6 (Rabbit polyclonal) | Yelagandula et al., 2014 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP | |
| Antibody | anti-H2A.W.7 (Rabbit polyclonal) | Lorković et al., 2017 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP | |
| Antibody | anti-H3 (Rabbit polyclonal) | Abcam | Cat# ab1791, RRID:AB_302613 | WB: 0,5 μg/ml 5 μg per ChIP |
| Antibody | anti- H3K36me3 (Rabbit polyclonal) | Abcam | Cat# ab9050, RRID:AB_306966 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP |
| Antibody | anti-H3K27me3 (Rabbit polyclonal) | Millipore | Cat# 07–449, RRID:AB_310624 | WB: 1 μg/ml 5 μg per ChIP |
| Antibody | anti-H3K4me3 (Rabbit polyclonal) | Abcam | Cat# ab8580, RRID:AB_306649 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP |
| Antibody | anti-H3K4me1 (Rabbit polyclonal) | Abcam | Cat# ab8895, RRID:AB_306847 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP |
| Antibody | anti-H3K27me1 (Rabbit polyclonal) | Millipore | Cat# 17–643, RRID:AB_1587128 | WB: 1 μg/ml 5 μl per ChIP 20 μl per IP |
| Antibody | anti-H1 (Rabbit polyclonal) | Agrisera | AS11 1801 | 5 μg per ChIP |
| Antibody | anti-H4K20me1 (Rabbit polyclonal) | Abcam | Cat# ab9051, RRID:AB_306967 | 5 μg per ChIP |
| Antibody | anti-H3K9me1 (Rabbit polyclonal) | Abcam | Cat# ab8896, RRID:AB_732929 | WB: 1 μg/ml 5 μg per ChIP 10 μg per IP |
| Antibody | anti-H3K9me2 (Mouse monoclonal) | Abcam | Cat# ab1220, RRID:AB_449854 | WB: 1 μg/ml 5 μg per ChIP |
| Antibody | anti-H3K9ac (rabbit polyclonal) | Millipore | Cat# 17–615, RRID:AB_1163437 | WB: 1 μg/ml |
| Antibody | anti-H3K18ac (rabbit polyclonal) | Abcam | Cat# ab1191, RRID:AB_298692 | WB: 1 μg/ml |
| Antibody | anti-H3K23ac (rabbit polyclonal) | Abcam | Cat# ab47813, RRID:AB_880444 | WB: 1 μg/ml |
| Antibody | anti-H3K27ac (rabbit polyclonal) | Abcam | Cat# ab4729, RRID:AB_2118291 | WB: 1 μg/ml |
| Antibody | anti-H3K122ac (rabbit polyclonal) | Abcam | Cat# ab33309, RRID:AB_942262 | WB: 1 μg/ml |
| Antibody | anti-H3K27me2 (rabbit polyclonal) | Abcam | Cat# ab24684, RRID:AB_448222 | WB: 1 μg/ml |
| Antibody | anti-H3K36me2 (rabbit polyclonal) | Abcam | Cat# ab9049, RRID:AB_1280939 | WB: 1 μg/ml |
| Antibody | anti-HA (Rat monoclonal) | Roche | Cat# 11867423001, RRID:AB_390918 | WB: 0,5 μg/ml |
| Antibody | Rabbit IgG (monoclonal) | Abcam | Cat# ab171870, RRID:AB_2687657 | 10 μg per IP |
| Commercial assay or kit | Nugen Ovation Ultralow V2 DNA-Seq library prep kit | NuGen | Cat# 0344 | |
| Commercial assay or kit | NEBNext Ultra II DNA library prep kit for Illumina | New England Biolabs | Cat# E7645L | |
| Commercial assay or kit | Dynabeads Protein A | Invitrogen | Cat# 10746713 | Used for ChIP |
| Commercial assay or kit | Protein A Mag Separose | GE Healthcare (Cytiva) | Cat# 28951378 | Used for IP |
| Commercial assay or kit | Anti-HA Affinity matrix | Roche | Cat# 11815016001 | Used for IP |
| Software, algorithm | ChromHMM | Ernst and Kellis, 2012; Ernst and Kellis, 2017 | RRID:SCR_018141 | |
| Software, algorithm | Trim Galore | DOI:10.5281/zenodo.5127898. | RRID:SCR_011847 | |
| Software, algorithm | Bowtie 2 | Langmead and Salzberg, 2012 | RRID:SCR_016368 | |
| Software, algorithm | Picard | broadinstitute.github.io/picard/ | RRID:SCR_006525 | |
| Software, algorithm | Deeptools | Ramírez et al., 2016 | RRID:SCR_016366 |
Additional files
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Supplementary file 1
Mapping statistics.
The file includes output statistics for mapping and trimming of all data included in the manuscript.
- https://cdn.elifesciences.org/articles/87714/elife-87714-supp1-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/87714/elife-87714-mdarchecklist1-v1.docx
