Supplemental Material for Klocko et al., 2018

<div>Figure S1 shows aberrant cytosine methylation in <i>dim-1</i> strains.</div><div>Figure S2 shows the complementation of a <i>dim-1</i> strain with an ectopic copy of gene NCU06484.</div><div>Figure S3 shows the phenotypic characterization of a <i>dim-1</i> strain, as this strain has changes in cytosine methylation, including the loss of cytosine methylation in constitutive heterochromatic regions and a gain in cytosine methylation in intergenic regions.</div><div>Figure S4 shows the cytosine (detected by bisulfite-sequencing) and histone methylation (as H3K9me3; detected by ChIP-sequencing) across all seven chromosomes of <i>Neurospora crassa</i>.</div><div>Figure S5 shows how the new cytosine methylation in a <i>dim-1</i> strain requires the DIM-2 DNA methyltransferase.</div><div>Figure S6 shows how an ectopic copy of the dim-2 gene does not rescue the loss of cytosine methylation phenotype in constitutive heterochromatic regions.</div><div>Figure S7 shows how the new cytosine methylation peaks in <i>dim-1</i> intergenic regions does not require the action of small RNAs produced by the ERI-1 helicase.</div><div>Figure S8 shows average enrichment profiles of H3K9me3 ChIP-sequencing replicate data across traditional constitutive heterochromatic regions, all regions gaining cytosine methylation in a <i>dim-1</i> strain, or just the neo-heterochromatic regions that only gain cytosine methylation in a <i>dim-1</i> strain.</div><div>Figure S9 shows how neo-heterochromatin requires the histone methyltransferase DIM-5</div><div>Figure S10 shows the affect of the <i>dim-1</i> strain on heterochromatic silencing.</div><div>Figure S11 shows the minimal changes to facultative heterochromatin, marked by H3K27me2/3, in a <i>dim-1</i> strain.</div><div>Figure S12 shows the growth rate of a <i>dim-1</i> strain.</div><div>Figure S13 shows a possible correlation that genes that gain of cytosine methylation in a <i>dim-1</i> strain are some of the most highly expressed in Neurospora. <br></div><div>Figure S14 shows the replicate analysis, using average enrichment profiles that use different reference points, of micrococcal nuclease sequencing experiments.<br></div><div>Figure S15 shows that an ectopic copy of the histone H3 gene does not rescue the cytosine methylation phenotype in a <i>dim-1</i> strain.</div><div>Figure S16 shows the changes in nucleosome positioning in genes that are up-regulated, down-regulated, and unchanged in a <i>dim-1</i> strain.</div><div>Figure S17 shows a control experiment for average enrichment profiles of nucleosome data: if random reference points are used, no periodicity is observed.</div><div>Figure S18 shows the proteins that interact with DIM-1, as determined by mass spectrometry. <br></div><div>Figure S19 show the proteins that interact with NCU00856, which is an interacting partner with DIM--1, and how the loss of NCU00856 does not cause a cytosine methylation phenotype.</div><div>Figure S20 shows the characterization of DIM-1 localization through DamID, including several genomic regions that were examined for DIM-1-DAM localization and how the removal of conserved domains from DIM-1 affected protein levels and localization.</div><div>File S1 shows an alignment of the DIM-1 primary structure with other orthologous proteins, and the associated E-values of those alignments.</div><div>File S2 provides the genes that are up- and down-regulated in dim-1 strains, the peak call files of H3K9me3, H3K27me2/3, and cytosine methylation, and the list of 1001 unchanged genes used as a control.</div><div>File S3 provides the python script to re-order the data within heatmaps so each heatmap is directly comparable.</div><div>Table S1 provides a list of strains used in this study.</div><div>Table S2 provides a list of oligos used in this study.<br></div><div><br></div>