Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Austria
- Department of Genetics, University of Leicester, United Kingdom
Figures
Figure 1 with 4 supplements
Chromatin accessibility is extensively reprogrammed in pollen.
(A) Schematic of Arabidopsis pollen development. Microspores divide asymmetrically to produce a vegetative cell nucleus (VN, green) and germ cell nucleus (GN, purple). While the vegetative cell …
Figure 1—figure supplement 1
Isolation of key cell types across Arabidopsis pollen development.
(A) Expression of ProVCK:NTF in mature Arabidopsis pollen, which specifically marks the vegetative cell nucleus (VN). A corresponding differential interference contrast (DIC) image is shown …
Figure 1—figure supplement 2
Transcriptomic profiling performed in this study.
(A) Table summarising the statistics of the RNA-seq libraries sequenced in this study. (B) Pearson cross-correlation matrix of the RNA-seq data sets generated in this study alongside sperm RNA-seq …
Figure 1—figure supplement 3
ATAC-seq profiling performed in this study.
(A) Table summarising the statistics of the ATAC-seq libraries sequenced in this study. (B) Spearman cross-correlation matrix of the pollen ATAC-seq data sets alongside published profiles from …
Figure 1—figure supplement 4
ATAC-seq profiling across Arabidopsis pollen development.
(A) Distribution of genomic features associated with ATAC-seq peaks recovered from nuclei of microspores (MN), germ cells (GN), sperm (SN), and vegetative cells (VN). (B) Distribution of ATAC-seq …
Figure 2 with 1 supplement
Pericentromeric sequences gain chromatin accessibility in the VN.
(A) Distribution of accessible chromatin region (ACR) density over the five Arabidopsis chromosomes calculated in 10 kb bins. Pericentromeric regions are indicated with grey shading. (B) Levels of …
Figure 2—figure supplement 1
DEMETER (DME) demethylates accessible chromatin uniformly across the VN.
(A) Genome browser view of the ATAC-seq data sets over a TE-rich pericentromeric region of chromosome 2. Tracks represent the levels of H3K9me2 in leaf (log2 ChIP-seq enrichment relative H3) and the …
Figure 3 with 2 supplements
DEMETER (DME) demethylates predicted TF binding sites in accessible chromatin.
(A and B) Relative proportion of VN-specific accessible chromatin regions (ACRs) (A) and common ACRs (B) that overlap with cytosines demethylated by DME in the VN. (C and D) Averaged metaplots …
Figure 3—figure supplement 1
Differential methylated region (DMR) analysis between VN from wild-type (WT) and dme-2/+ mutant pollen.
(A–C) Violin plots showing weighted DNA methylation rates of DMRs in CG (A), CHH (B), and CHG (C) context. Each overlaid boxplot indicates minimum and maximum values as well as 25th, 50th, and 75th …
Figure 3—figure supplement 2
DEMETER (DME) demethylates predicted TF binding sites specifically in the VN.
(A–J) DNA methylation level at predicted binding sites within DME-targeted accessible chromatin regions (ACRs) for the remaining 10 methylation-sensitive TFs shown in Figure 4E – bZIP28 (A), WRKY27 …
Figure 4
DEMETER (DME) activity regulates the expression of pollen tube-related genes.
(A) Distribution of genomic features associated with DME-targeted accessible chromatin regions (ACRs). (B) Expression status of genes lying in the vicinity (<900 bp) of a DME-targeted ACR. Genes …
Figure 5
Chromatin accessibility in sperm forecasts sporophytic development.
(A) Sperm ATAC-seq profiles reflect the reprogrammed state of sporophytic H3K27me3 target genes. Plotted are averaged levels of leaf H3K27me3 and sperm H3K4me3 (log2 ChIP-seq enrichment relative to …
Author response image 1
Additional files
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Supplementary file 1
Pollen ATAC-seq accessible chromatin regions (ACRs) detailed in this study.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp1-v2.txt
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Supplementary file 2
Differentially hyper-methylated cytosines (DMCs) in vegetative cell nucleus (VN) from dme-2/+ pollen compared to wild type (WT) described in this study.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp2-v2.txt
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Supplementary file 3
DEMETER (DME)-targeted accessible chromatin regions (ACRs) described in this study.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp3-v2.txt
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Supplementary file 4
Differential gene expression analysis of wild-type (WT) and dme-2/+ pollen.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp4-v2.txt
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Supplementary file 5
Pollen-tube related genes directly regulated by DEMETER (DME)-dependent demethylation.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp5-v2.txt
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Supplementary file 6
H3K27me3-repressed accessible chromatin regions (ACRs) described in this study.
- https://cdn.elifesciences.org/articles/61894/elife-61894-supp6-v2.txt
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Transparent reporting form
- https://cdn.elifesciences.org/articles/61894/elife-61894-transrepform-v2.docx
