Supplemental Figure 1.

Transcription

1 Supplemental Data. Charron et al. Dynamic landscapes of four histone modifications during de-etiolation in Arabidopsis. Plant Cell (2009) /tpc Supplemental Figure 1. Immunodetection of acetylated and tri-methylated histone H3. Modified histones from D and D to L seedlings were analyzed by Western blot probed with antibodies against H3K9ac, H3K9me3, H3K27ac, H3K27me3 and H3. Portion of a Coomassie blue-stained gel is shown as loading control (Bottom panel).

2 Supplemental Figure 2. H3K9ac, H3K9me3, H3K27ac, and H3K27me3 Mark Different Levels of Gene Expression. (A) Distribution of H3K9ac, H3K9me3, H3K27ac, and H3K27me3 within five groups of genes with different levels of expression intensity in D seedlings. (B) Distribution of H3K9ac, H3K9me3, H3K27ac, and H3K27me3 within five groups of genes with different levels of expression intensity in D to L seedlings. Genes were sorted into bins based on increasing expression intensity from the analysis presented in figure 1. The y-axis shows the averaged ratios between the signals from the samples enriched for each modification and the signal from nucleosomal DNA.

3 Supplemental Figure 2. (cont d) (C) Distribution of H3K9ac, H3K9me9, H3K27ac, and H3K27me3 signals within TE genes. The y-axis shows the averaged signals from the samples enriched for each modification (not a ratio). (D, WT plants dark grown for 5 days; D to L, WT plants dark grown for 4.75 days and transfer to white light for 6 hours). All genes were aligned at their transcription start sites (TSS). The y-axis shows the averaged ratios between the signals from the samples enriched for each modification and the signal from nucleosomal DNA. Gene regions include a 1kb promoter.

4 Supplemental Figure 3. Validation of H3K9ac ChIP-chip Results by ChIP-PCR from four Independently Prepared Biological ChIP Replicates. ChIP-chip results of two genomic regions: HY5 (At5g11260), CAB4 (At3g47470) are shown (top). A schematic representation of each gene (rectangles = exons and lines = introns) within these regions is shown (middle). Red boxes with arrows indicate direction of transcription. Grey boxes represent regions assayed by ChIP-PCR (see Supplemental Table 3 for primer sequences). ChIP-PCR results are shown as the fold of enrichment of H3K9ac over nucleosomal DNA (bottom). Error bars represent SE. Primer sequences are presented in Supplemental Table 1.

5 Supplemental Figure 4. Additional validation of H3K9ac ChIP-chip Results by ChIP- PCR from four Independently Prepared Biological ChIP Replicates. ChIP-chip results of genomic regions within strictosidine synthase genes (At3g57010, At3g57020, At3g57030) are shown (top). A schematic representation of each gene (rectangles = exons and lines = introns) within these regions is shown (middle). Red boxes with arrows indicate direction of transcription. Fold changes represent gene expression differences between dark grown WT seedlings transferred to white light (D to L) and dark grown WT seedlings (D). Grey boxes represent regions assayed by ChIP-PCR (see Supplemental Table 3 for primer sequences). ChIP-PCR results are shown as the fold of enrichment of H3K9ac over nucleosomal DNA (bottom). Error bars represent SE. Primer sequences are presented in Supplemental Table 1.

6 Supplemental Figure 5. Validation of H3K27ac ChIP-chip Results by ChIP-PCR from four Independently Prepared Biological ChIP Replicates. ChIP-chip results of three genomic regions: PP2C (At2g25070), hypothetical protein (At3g15095), putative DNA helicase (At5g67630) are shown (top). A schematic representation of each gene (rectangles = exons and lines = introns) within these regions is shown (middle). Red boxes with arrows indicate direction of transcription. Grey boxes represent regions assayed by ChIP-PCR (see Supplemental Table 3 for primer sequences). ChIP-PCR results are shown as fold enrichment of H3K27ac over nucleosomal DNA (bottom). Error bars represent SE. Primer sequences are presented in Supplemental Table 1.

7 Supplemental Figure 6. Validation of H3K27me3 ChIP-chip Results by ChIP-PCR from four Independently Prepared Biological ChIP Replicates. ChIP-chip results of three genomic regions: GA2ox7 (At1g50960), GA3ox2 (At1g80340), hypothetical protein (At5g66440) are shown (top). A schematic representation of each gene (rectangles = exons and lines = introns) within these regions is shown (middle). Red boxes with arrows indicate direction of transcription. Green boxes represent regions assayed by ChIP-PCR (see Supplemental Table 3 for primer sequences). ChIP-PCR results are shown as fold enrichment of H3K27me3 over nucleosomal DNA (bottom). Error bars represent SE. Primer sequences are presented in Supplemental Table 1.

8 Supplemental Figure 7. Distribution of Four Histone Modifications within Arabidopsis Genes. (A) Distribution of H3K9ac, H3K9me9, H3K27ac, and H3K27me3 levels within non- TE genes. The y-axis shows the averaged ratios between the signals from the samples enriched for each modification and the signal from nucleosomal DNA. (B) Distribution of H3K9ac, H3K9me9, H3K27ac, and H3K27me3 levels within TE genes. The y-axis shows the averaged ratios between the signals from the samples enriched for each modification and the signal from nucleosomal DNA. (C) Distribution of H3K9ac, H3K9me9, H3K27ac, and H3K27me3 signals within non- TE genes. The y-axis shows the averaged signals from the samples enriched for each modification (not a ratio). (D) Distribution of H3K9ac, H3K9me9, H3K27ac, and H3K27me3 signals within TE genes. The y-axis shows the averaged signals from the samples enriched for each modification (not a ratio).

9 Supplemental Figure 8. Histone Modifications in Gene Promoter and Body Regions. (A) Numbers of " promoter", " body" and "promoter and body" modified non-te genes (D, WT plants dark grown for 5 days; D to L, WT plants dark grown for 4.75 days and transfer to white light for 6 hours).

10 Supplemental Figure 8 (cont d) (B) Association between the expression levels and the proportions of "promoter", "body," and "both promoter and body" modified genes in D seedlings. (C) Association between the expression levels and the proportions of "promoter", "body, and "promoter and body" modified genes in D to L seedlings. The x-axis shows the expression level (log2) calculated from the analysis presented in figure 1. For B and C, the x-axis shows the expression level (log2) calculated from the analysis presented in Figure 1. The y-axis shows the percentage of genes in the indicated category containing the specified modification.

11 Supplemental Figure 9. Acetylation of promoter regions does not increase gene expression levels. Distribution of H3K9ac levels within non-te genes modified over (A) their promoter or (B) body regions in D to L seedlings (WT plants dark grown for 4.75 days and transfer to white light for 6 hours). Non-TE genes were sorted into bins based on increasing expression intensity from the analysis presented in Figure 1 (2-4, lowest; 4-6, low; 6-8, high; >8, highest). All genes were aligned at their transcription start sites (TSS). The y-axis shows the averaged ratios between the signals from the samples enriched for H3K9ac and the signal from nucleosomal DNA. Gene regions include a 2kb promoter. Similar results were obtained for D and cop1-4 seedlings as well as for H3K27ac.

12 Supplemental Figure 10. Comparison of identified target genes with previously published datasets. (A) Venn diagrams showing the overlap of non-te genes targeted by H3K27me3 identified in this study with datasets from Zhang et al. (2007) and Turck et al (2007). (B) Venn diagrams showing the overlap of non-te genes targeted by H3K9ac identified in this study with the dataset from Zhou et al. (unpublished). (C) Venn diagrams showing the overlap of non-te genes targeted by H3K9me3 identified in this study with dataset from Turck et al (2007). D, WT Arabidopsis grown in darkness; D to L, WT Arabidopsis grown in darkness and transfer to light conditions; LD, WT Arabidopsis grown under long day conditions; LL, WT Arabidopsis grown in continuous light (LL). Only target genes from chromosome 4 (Chr4) were used for comparaison with the Turck et al. (2007) dataset.

13 Supplemental Figure 11. Magnification of Figure 6B. Overview of photosynthesis gene expression by cluster display. D to L / D, dark to light versus dark. The color scale is shown at the bottom.

14 Supplemental Table 1. PCR Primers Used for Validation of Modified Regions Regions no. Chr Forward Primer Reverse Primer in Supplemental Figure TCGATCAGGCGAGAGAGAGAGGGAAA CGGCTAAAATCCACCCACGTTCCA 2 5 CCAAACAACCCCATCACGCAACC GGCGAGTGCCGGAGTTTGGA 3 5 TCTTTTCTGAGCAGACCATCTCTGTTGCAT TGCTTCGTGACCCGCCTCCA 4 3 CTAGCCAGACCCCAGAAAACAAGATACATAAGC GGTCAAGATAATAGTCAATCTCATCATTTGCTCCA 5 3 TTCTTTCCTCAATCAGGTTGGCTTATATGTGTG TGTTGAACCGTTGTAGCTCCATGAACAA 6 3 CGACCCGAGAACCCGGCACT TCTCCTCCGTCAAATCAACCACGTCA in Supplemental Figure TGAAGTCCAAATAATTGCCAAATTGAATTAAACG GGTACGTTTTAAGTGCGATCGATTGGTTATTG 2 3 GGCGGTGATCGGCGTCAGAA CGACGTGTGTAACGTTTCTTGTGTCCTAAATCA 3 3 CCCCTTGGTTGGCAAACATAACTTTACGAC TGGTGAATAAAGAGATAACTGTTCGAGTCATGAGG 4 3 CAGCCGGAACGGCAAACCAA TGCATGGATTCGTCGCAGCATTT 5 3 TCGGCCAAGCCTCCCTCTGG TCAGCCAAATCCTTGTGGCTTGTCA 6 3 TGGTCATGGTGATTGGTGCCTTGG GGGCCGGCAAATGGGCTTC 7 3 TGCAAATGGGCGAGCACACTCC TGGAATTGAAATGTTTGCTCAGTGTTTTGTCA in Supplemental Figure TCGGAGAACTTAGGTATGTACCCATCGCTTT TTGTGTAAGATTCTGATTGGTTTGATGGTTTCA 2 2 GCTCGGCTCATCTTCGCTTGG TGTTCCTGTCTTGGTCAGTGACATTGG 3 3 TGCGTGTCTGAGTGTTTGTGTTTTTGG TCACGATTTAGTTTTGTTGCGTTTTTGAGG 4 3 GCAGAAGCTCCTTTGCCTTCAAATCC CGTCTCAGCCACCGCCACAA 5 5 TCCCTGACTTGGAAGCAACACCA CGATTGCAATGGGTATGGCGAAA 6 5 GCCACCACAAGGATTGGTGACATT TGCCCTTTTCACTGGCGATACTGG in Supplemental Figure TTTCTCGATCGGGATATTCTCTGTTGC CCAAATATAAAGATTTCAATGGGCCAACG 2 1 TCATGTACTATAGCTTTACATGGCTTCTCAACCTC TCGATCACAGGAAGCTTTATGCCTGA 3 1 TTCAGAGAGTACAAAGAGCAGAGTGAACATGA TGTTACATCGATTTTTATTAGACCTTGCCTTAAACA 4 1 GCAAGGTATTGTTTCCAAGTGAGAGATGG TCGGTGACTTGCTCCACATTTTAACCA 5 1 AGGTGGTGGCTGGGCCAGAG GGCGTCCCCTCGCGACTTCT 6 5 CGCCGCGTTTAGATCGTTGGT GCAGCTGCCGCCAATACATTCC 7 5 GCTCCTCCACCACCACCAGTTCC AACGAATCTTCATCGATCAAACTCATCAAA