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Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome

Emanuela Sani13, Pawel Herzyk1, Giorgio Perrella1, Vincent Colot2 and Anna Amtmann1*

Author Affiliations

1 Institute of Molecular, Cell and Systems Biology (MCSB), College of Medical, Veterinary & Life Sciences (MVLS), University of Glasgow, Glasgow G128QQ, UK

2 Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris, F-75005, France

3 Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK

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Genome Biology 2013, 14:R59  doi:10.1186/gb-2013-14-6-r59

Published: 14 June 2013

Additional files

Additional file 1:

Additional Figures and Table. Figure S1. Appearance of primed and non-primed plants after long-term salt stress. Plants had been treated with either 0 (control, not primed, left), 50 mM (primed, center), or 100 mM NaCl (primed, right) for 24 h at seedling stage and subsequently grown for 10 days in hydroponics without salt. The solution was then supplemented with 80 mM or not (control, no salt) and plants photographed 10 days later. No difference in salt tolerance was apparent between primed and non-primed plants. Figure S2. Example of a successful ChIP quality control. Based on published histone methylation profiles primers were designed to amplify regions that are enriched (positive controls) or devoid (negative controls) of H3K4me2, H3K4me3, H3K9me2, or H3K4me3. (Note that no region was found that was exclusively associated with H3K4me2.) ChIP samples from roots (R) or shoots (S) of primed (50) or non-primed (C) plants obtained with antibody against H3K9me2 (A), H3K27me3 (A), H3K4me2 (M2), or H3K4me3 (M3) were used as template as well as ChIP input DNA (I) and ChIP without antibodies (NA). For primer pairs see Table S3. Figure S3. Genome-wide histone modification landscapes in primed and non-primed plants. Genome-wide profiles of read counts for H3K4me2 (green), H3K4me3 (red), H3K9me2 (purple), and H3K27me3 (blue) in roots samples of primed (PR) and non-primed (CR) plants displayed in the Integrated Genome Browser (IGB). Figure S4. Kinetics of H3K27me3 and mRNA after salt application. Relative enrichment of H3K27me3 (black bars, left y-axis) and mRNA levels (open bars, right y-axis) of nine genes in roots of A. thaliana seedlings were determined by qPCR over a time course of 8 h (x-axis) after application of 50 mM NaCl (priming treatment). H3K27me3 levels (left y-axis) were normalized to ChIP input and to reference region in At5g56920. mRNA levels (right y-axis) were normalized to reference gene RpII. For details see main text and Figure 6D. Table S1. Chromosome coordinates of priming-induced H3K27me3 differences. Table S2. Expression levels of selected genes in root RNA 4 h after second salt treatment. Table S3. Sequences of primers used in this study

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Additional file 2:

Enrichment of functional terms among genes with mapped differences in H3K4me3 and H3K27me3 as determined by DAVID. Enrichment calculated over genes with mapped islands in control (background C) or primed samples (background P). Upstream and downstreams sequences included were either 100 bp or 100 pb.

Format: XLS Size: 171KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Reads200_CRH3K4me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CRH3K4me2.

Format: WIG Size: 13.1MB Download file

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Additional file 4:

Reads200_CRH3K4me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CRH3K4me3

Format: WIG Size: 12.5MB Download file

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Additional file 5:

Reads200_CRH3K9me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CRH3K9me2

Format: WIG Size: 13.3MB Download file

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Additional file 6:

Reads200_CRH3K27me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CRH3K27me3

Format: WIG Size: 13.4MB Download file

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Additional file 7:

Reads200_CSH3K4me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CSH3K4me2

Format: WIG Size: 13.1MB Download file

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Additional file 8:

Reads200_CSH3K4me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CSH3K4me3

Format: WIG Size: 11.3MB Download file

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Additional file 9:

Reads200_PRH3K4me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PRH3K4me2

Format: WIG Size: 12.9MB Download file

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Additional file 10:

Reads200_PRH3K4me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PRH3K4me3

Format: WIG Size: 11.4MB Download file

Open Data

Additional file 11:

Reads200_PRH3K9me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PRH3K9me2

Format: WIG Size: 13.7MB Download file

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Additional file 12:

Reads200_PRH3K27me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PRH3K27me3

Format: WIG Size: 12.5MB Download file

Open Data

Additional file 13:

Reads200_PSH3K4me2.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PSH3K4me2

Format: WIG Size: 13MB Download file

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Additional file 14:

Reads200_PSH3K4me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h PSH3K4me3

Format: WIG Size: 11.3MB Download file

Open Data

Additional file 15:

Reads200_TendaysCRH3K27me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 24h CRH3K27me3

Format: WIG Size: 8.3MB Download file

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Additional file 16:

Reads200_TendaysPRH3K27me3.wig. WIG file containing sequence read counts over 200 bp windows in sample 10d PRH3K27me3

Format: WIG Size: 9.5MB Download file

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Additional file 17:

Islands_CRH3K4me2-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CRH3K4me2. (G: optimized gap size in bp.)

Format: BED Size: 539KB Download file

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Additional file 18:

Islands_CRH3K4me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CRH3K4me3. (G: optimized gap size in bp.)

Format: BED Size: 895KB Download file

Open Data

Additional file 19:

Islands_CRH3K9me2-G400.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CRH3K9me2. (G: optimized gap size in bp.)

Format: BED Size: 74KB Download file

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Additional file 20:

Islands_CRH3K27me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CRH3K27me3. (G: optimized gap size in bp.)

Format: BED Size: 214KB Download file

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Additional file 21:

Islands_CSH3K4me2-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CSH3K4me2. (G: optimized gap size in bp.)

Format: BED Size: 556KB Download file

Open Data

Additional file 22:

Islands_CSH3K4me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h CSH3K4me2. (G: optimized gap size in bp.)

Format: BED Size: 894KB Download file

Open Data

Additional file 23:

Islands_PRH3K4me2-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PRH3K4me2. (G: optimized gap size in bp.)

Format: BED Size: 522KB Download file

Open Data

Additional file 24:

Islands_PRH3K4me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PRH3K4me3. (G: optimized gap size in bp.)

Format: BED Size: 913KB Download file

Open Data

Additional file 25:

Islands_PRH3K9me2-G400.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PRH3K9me2. (G: optimized gap size in bp.)

Format: BED Size: 82KB Download file

Open Data

Additional file 26:

Islands_PRH3K27me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PRH3K27me3. (G: optimized gap size in bp.)

Format: BED Size: 251KB Download file

Open Data

Additional file 27:

Islands_PSH3K4me2-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PSH3K4me2. (G: optimized gap size in bp.)

Format: BED Size: 562KB Download file

Open Data

Additional file 28:

Islands_PSH3K4me3-G600.bed. BED file containing coordinates of islands as determined by SICER software in sample 24h PSH3K4me3. (G: optimized gap size in bp.)

Format: BED Size: 724KB Download file

Open Data

Additional file 29:

slands_TendaysCRH3K27me3-G400.bed. BED file containing coordinates of islands as determined by SICER software in sample 10d CRH3K27me3. (G: optimized gap size in bp.)

Format: BED Size: 152KB Download file

Open Data

Additional file 30:

Islands_TendaysPRH3K27me3-G400.bed. BED file containing coordinates of islands as determined by SICER software in sample 10d PRH3K27me3. (G: optimized gap size in bp.)

Format: BED Size: 199KB Download file

Open Data

Additional file 31:

Differences_PvsC_RH3K4me2.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h RH3K4me2 samples.

Format: BED Size: 18KB Download file

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Additional file 32:

Differences_PvsC_RH3K4me3.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h RH3K4me3 samples.

Format: BED Size: 35KB Download file

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Additional file 33:

Differences_PvsC_RH3K9me2.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h RH3K9me2 samples.

Format: BED Size: 13KB Download file

Open Data

Additional file 34:

Differences_PvsC_RH3K27me3.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h RH3K27me3 samples.

Format: BED Size: 182KB Download file

Open Data

Additional file 35:

Differences_PvsC_SH3K4me2.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h SH3K4me2 samples.

Format: BED Size: 1KB Download file

Open Data

Additional file 36:

Differences_PvsC_SH3K4me3.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 24h SH3K4me3 samples.

Format: BED Size: 1KB Download file

Open Data

Additional file 37:

Differences_PvsC_TendaysRH3K27me3.bed. BED file containing coordinates for differences determined by CHIPDIFF software between primed (P) and non-primed (C) 10d RH3K27me3 samples.

Format: BED Size: 12KB Download file

Open Data

Additional file 38:

TAIR9genes.bed. BED file containing coordinates of A. thaliana genes.

Format: BED Size: 3.1MB Download file

Open Data