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. 2017 May 17;8:15120.
doi: 10.1038/ncomms15120.

Temporal Dynamics of Gene Expression and Histone Marks at the Arabidopsis Shoot Meristem During Flowering

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Free PMC article

Temporal Dynamics of Gene Expression and Histone Marks at the Arabidopsis Shoot Meristem During Flowering

Yuan You et al. Nat Commun. .
Free PMC article

Abstract

Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering.

Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Establishment of the INTACT system for the meristem.
(a,b) Detection of biotinylation and (d,e) expression of the floral marker gene AP1 at the meristem of the INTACT line before (a,d) and 3 days after (b,e) the shift to LD. Scale bar, 50 μm. (c) Semi-quantitative RT–PCR detecting expression of STM, CLV3 and FD in the total nuclei from the samples enriched for shoot apical region by manual dissection (input) and in the nuclei isolated by INTACT from the meristem (INTACT). (f) Quantitative RT–PCR of SOC1 (light grey) and AGL24 (dark grey) in the nuclei from the meristem before (0), and 1, 2 and 3 days after the shift to LD. Error bars, values of two biological replications.
Figure 2
Figure 2. Differential gene expression in the meristem during flowering.
(ah) Expression (counts of reads) of marker genes for the meristem (a), leaf primordia (b), flower primordia (c), circadian clock (d), flowering time (e), stem cell (f), translation (g) and lateral organ boundary (h) at the SAM before (blue), and 1 (green), 2 (red) and 3 (purple) days after the shift to LD. Error bars,±s.e. based on four biological replicates; *P<0.05, **P<0.01 (Deseq2 P values corrected for multiple testing using the Benjamini-Hochberg method). (i) Biological GO functions enriched for differentially regulated genes with increased (red) and decreased (blue) expression. Only significantly enriched GO terms (P<0.05) are reported.
Figure 3
Figure 3. Positive correlation between H3K4me3 and expression.
(a) Normalized H3K4me3 signal on protein-coding genes in 0 LD samples between −4 kb and +8 kb around the TSS. Genes ordered according to their expression level (regularized logarithm (rlog) of counts, red line). (b) Distribution of expression of protein-coding genes in 0 LD samples in relation to the position of the H3K4me3 marks. (c) Protein-coding genes with significant differences in H3K4me3 signal between 0 LD and 3 LD samples. Red and blue indicate the direction and significance of gain and loss of H3K4me3, respectively. Genes ordered according to significance (−Log10(P value)) of changes in expression (green line). (d) Key biological processes enriched in genes with significant H3K4me3 changes. Colour key indicates the significance (−Log10(P value)) of the enriched GO terms that gained (red) and lost (blue) H3K4me3, respectively. Only significantly enriched GO terms (P<0.05; fold-change>2) are shown.
Figure 4
Figure 4. Examples of H3K4me3 and H3K27me3 dynamics at the SAM during the floral transition.
(ai) Integrative Genomics Viewer traces of AP1 (a), JAG (b), FT (c), STM (d) KNAT2 (e), KNAT6 (f), PTL (g), FLC (h), DAL (i), RPL27C (j), SOC1 (k), SNZ (l). H3K4me3, H3K27me3 and H3 signals are depicted in blue, green and red, respectively. Horizontal bars indicate regions and signals of significant enrichment of H3K4me3 and H3K27me3 (according to analysis in MACS2).
Figure 5
Figure 5. Profiles of H3K4me3 and H3K27me3 marks at the SAM.
(a) Distribution of normalized H3K4me3 and H3K27me3 signal across the body (±1 kb) of protein-coding genes in 0 LD sample. Regions upstream of the TSS (1 kb) and downstream of TTS (+1 kb) were each divided into 10 bins of length 100 bp. Gene bodies were normalized to account for differences in gene length and divided into 50 bins of equal width. Genes sorted based on levels of expression (red line), and genes with no detectable expression were sorted by H3K27me3 levels. (b) Distribution of expression of protein-coding genes in 0 LD samples in relation to the position of the H3K4me27 marks. (c) Protein-coding genes with significant differences in H3K27me3 signal between 0 and 3 LDs samples. Red and blue indicate the direction and significance of gain and loss of H3K27me3, respectively. Genes ordered according to significance (−Log10(P value)) of changes in expression (green line).
Figure 6
Figure 6. Enrichment of H- and E- states at the SAM.
(a,b) Overlap of genes in H-state (a) and E-state (b) detected in 0 LD SAM and in whole-seedling samples. (c,d) Distribution of H3K4me3 and H3K27me3 marks across the gene body (±1 kb) of genes in H-state (c) and E-state (d) in 0 LD SAM (left) and the whole seedlings (right). Genes were ordered by expression in the meristem samples (red lines).
Figure 7
Figure 7. H- and E-state genes at the SAM during floral transition.
(a) Molecular GO functions enriched for H-state, E-state and H/E-state genes. Only significantly enriched GO terms (P<0.05, fold-change>1.5) are reported. (b) Matrix of chromatin state transitions from 0–3 LDs for non-overlapping (Non), H-state, and E-state genes, and genes with partial overlapping H3K27me3-H3K4me3 marks (K27>K4; K4>K27). Colours indicate the fraction of genes in a given category on 3 LD, starting from the 0 LD sample (n=number of genes in each category in the 0 LD sample).

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References

    1. Weigel D. & Jürgens G. Stem cells that make stems. Nature 415, 751–754 (2002). - PubMed
    1. Wilczek A. M. et al. . Effects of genetic perturbation on seasonal life history plasticity. Science 323, 930–934 (2009). - PubMed
    1. Kwiatkowska D. Flowering and apical meristem growth dynamics. J. Exp. Bot. 59, 187–201 (2008). - PubMed
    1. de Montaigu A. et al. . Natural diversity in daily rhythms of gene expression contributes to phenotypic variation. Proc. Natl Acad. Sci. USA 112, 905–910 (2015). - PMC - PubMed
    1. Corbesier L. et al. . FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030–1033 (2007). - PubMed

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