Science Advances

Supplementary Materials

This PDF file includes:

  • discussion S1. Comparisons with previous methylation studies in corals.
  • discussion S2. S. pistillata promoter methylation has no effect on gene expression.
  • discussion S3. Correlation of genic expression to methylation.
  • discussion S4. Validation of methylation patterns.
  • discussion S5. Differential expression and methylation of biomineralization genes.
  • fig. S1. Amplicon-specific bisulfite sequencing can accurately assay methylation levels of amplicons of interest.
  • fig. S2. Down-regulation of Ras and Ras guanine nucleotide exchange factors and up-regulation of Ras GTPase-activating proteins suggest a reduction in active Ras.
  • fig. S3. Differential expression of key genes was corroborated using RT-qPCR.
  • fig. S4. Distribution of CpGO/E (“CpG bias”) for genes in S. pistillata.
  • fig. S5. Multiple lines of evidence suggesting that promoter methylation does not influence expression patterns in S. pistillata.
  • fig. S6. Methylation patterns are strongly tissue-specific.
  • fig. S7. Effect of long-term pH stress on selected biomineralization-related genes.
  • table S1. Modeling transcriptional noise as a function of expression level and methylation state.
  • References (49–58)

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Other Supplementary Material for this manuscript includes the following:

  • data S1 (Microsoft Excel format). Trimming, mapping, and coverage calculations for WGBS reads.
  • data S2A (Microsoft Excel format). Differentially methylated genes at pH 7.2, relative to control.
  • data S2B (Microsoft Excel format). Differentially methylated genes at pH 7.4, relative to control.
  • data S2C (Microsoft Excel format). Differentially methylated genes at pH 7.8, relative to control.
  • data S3A (Microsoft Excel format). Enriched GO terms for differentially methylated genes at pH 7.2.
  • data S3B (Microsoft Excel format). Enriched GO terms for differentially methylated genes at pH 7.4.
  • data S3C (Microsoft Excel format). Enriched GO terms for differentially methylated genes at pH 7.8.
  • data S4A (Microsoft Excel format). Sequences and miscellaneous details of primers used in qPCR.
  • data S4B (Microsoft Excel format). Raw Ct values of qPCR experiment.
  • data S4C (Microsoft Excel format). ddCt approach for fold change calculations.
  • data S5A (Microsoft Excel format). Raw values of cell size measurements.
  • data S5B (Microsoft Excel format). Raw values of calyx size measurements.
  • data S5C (Microsoft Excel format). Raw values of porosity measurements.
  • data S6A (Microsoft Excel format). Enriched GO terms for all methylated genes.
  • data S6B (Microsoft Excel format). Enriched GO terms for highly methylated genes.
  • data S7 (Microsoft Excel format). Methylation levels measured via amplicon sequencing and WGBS.
  • data S8 (Microsoft Excel format). Results from tissue-specific amplicon sequencing.
  • data S9 (Microsoft Excel format). List of putative biomineralization-related genes in S. pistillata.

Download data S1 to S9

Files in this Data Supplement: