Supplemental Material for Anderson et al., 2018

Supplemental tables and figures for G3/2018/20028

TableS2.xlsx

<p>Table S2 from "Subtle perturbations of the maize methylome reveal genes and transposons silenced by CHROMOMETHYLASE or RNA-directed DNA methylation pathways" </p><p><br></p><p>Contains expression values, differential expression calls, list assignments, and DMR calls for all genes.</p

Effect of high CHG methylation or H3K9me2 over promoter on expression.

<p>(A) All maize genes were grouped into 5 groups: a subset of genes not expressed and then of the expressed genes, four quartiles of equal size increasing in expression level from 1 to 4 (gray). The relative proportion of genes containing TE insertions (dark blue), genes with high H3K9me2 (light blue) or high CHG in promoters (pink) in these five groups is shown. (B) Genes containing high levels of CHG or H3K9me2 over the transcription start site were identified and the overlap is shown (full list of genes in each category is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105267#pone.0105267.s008" target="_blank">Table S1</a>). (C) Relative level of CHG methylation or H3K9me2 in each subset of promoter regions.</p

DNA methylation and H3K9me2 levels of genic transposons.

<p>(A) An example of a transposable element insertion located within an intron of a maize gene is shown using Integrated Genome Viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105267#pone.0105267-Robinson1" target="_blank">[48]</a>. The H3K9me2 ChIP-seq read count is shown in red. The levels of CG, CHG and CHH methylation (per 100 bp tile) are shown in blue. (B) The average CG, CHG and CHH DNA methylation levels are shown for all TEs (orange), genic TEs (blue) and exons (maroon). (C) The average H3K9me2 read counts are shown for the same regions. (D) The profile of DNA methylation and H3K9me2 over genic TEs is shown.</p

Enrichment of DNA methylation and H3K9me2 over transposable elements.

<p>(A–B) Relative distance line plots of DNA methylation over transposable elements in maize and <i>Arabidopsis</i>. The plot in A shows the average enrichment for each type of DNA methylation of DNA transposons containing terminal inverted repeats (TIRs). The colors of the lines indicate the context of DNA methylation (black-CG; red-CHG; green-CHH) and type of line indicates the species (solid = maize; dashed = <i>Arabidopsis</i>). In (B) similar plots are shown for long terminal repeat (LTR) retrotransposons. (C) Plots of H3K9me2 abundance are shown for DNA transposons (purple) and retrotransposons (blue) in both maize (solid lines) and <i>Arabidopsis</i> (dashed lines). (D) The average level of DNA methylation or H3K9me2 is plotted for different sub-classes of transposable elements. The retrotransposons are divided into LINEs, RLG (gypsy-like), RLC (copia-like) and RLX (LTR elements of unknown class). The RLG, RLC and RLX elements are all split according to whether they exhibit evidence for spreading of H3K9me2 or DNA methylation in flanking regions as defined in Eichten et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105267#pone.0105267-Eichten3" target="_blank">[27]</a>. The DNA transposons are divided into five major families (DTA (<i>hAT</i>), DTC (<i>CACTA</i>), DTH (<i>PIF/Harbinger</i>), DTM (<i>Mutator</i>) and DTT (<i>Tc1/Mariner</i>)) and for two of these there are large families of “non-coding” elements that are indicated as “-nc”. The last three bars indicate the average levels for each modification 1 kb away from TEs, within exons or within introns. (E) The relative levels of H3K9me2 and CHH methylation are shown for each sub-family of transposons. The levels for TE flanking regions, exons and introns are also shown.</p

Genome-wide levels of DNA methylation and H3K9me2.

<p>(A) Average genome-wide DNA methylation levels in CG, CHG, and CHH sequence contexts. These numbers refer to the average DNA methylation level for all cytosines within this sequence context. Solid bars are maize DNA methylation and dashed bars are <i>Arabidopsis</i> DNA methylation (data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105267#pone.0105267-Baucom1" target="_blank">[34]</a>). (B) The proportion of 100 bp tiles across the maize genome containing different levels of DNA methylation is shown. (C–D) The average read number for H3K9me2 ChIP-seq was determined for 100 bp tiles in maize (C) or <i>Arabidopsis</i> (D) having varying levels of CHG and CHH methylation and is shown using a heat map to illustrate relative enrichment.</p

Demographics registered users’ research area (A), occupation (B), and genders (C).

Demographics registered users’ research area (A), occupation (B), and genders (C).</p

DE applications.

How they run, where they run, and popular applications. (PDF)</p

Glossary.

Frequently used abbreviations and acronyms with descriptions. (PDF)</p

Multiplier effects.

Only 25% of NSF awards which requested Letters of Collaboration (LOCs) mention “CyVerse” or “iPlant Collaborative” in their public abstract. Of the total awards that mention “CyVerse” or “iPlant Collaborative” 73% did not request LOCs.</p