Fig. 3

Comparative epigenomic analysis of S. pombe, unicellular and multicellular D. discoideum, and C. elegans identifies unicellular and multicellular signatures. a The 1000 most highly expressed genes at each life cycle stage display a higher degree of chromatin accessibility than the 1000 most lowly expressed genes at each life cycle stage. ****: p < 0.0001 as assessed by one-way ANOVA. b Representative integrative genomics viewer (IGV) tracks of H3K4me3 (orange), H3K27me3 (purple), ATAC-seq (red), and gene expression (navy) at srfA demonstrates increases in H3K4me3, decreases in H3K27me3, and increased chromatin accessibility at the promoters correlate with increases in gene expression of D. discoideum at four life cycle stages. c A Venn diagram displays the 2473 conserved genes in S. pombe, D. discoideum, and C. elegans. d PCA of orthologous genes illustrates that unicellular enriched gene expressions of D. discoideum cluster closer to S. pombe than to multicellular D. discoideum by the third principal component. e Single-cell RNA sequencing analysis of vegetative (blue), slug (yellow), and fruiting body (orange) cells reveals unique gene expression signatures of different stage D. discoideum. Uniform manifold approximation and projection (UMAP) is displayed for visual representation. f Single-cell RNAseq expression correlates highly with bulk RNAseq expression as exemplified by 67 “unicellular” genes and 52 “multicellular” genes. The 67 genes represented are accessible and expressed in unicellular D. discoideum and S. pombe but not in multicellular D. discoideum and C. elegans and the 52 genes represented display the opposite accessibility and expression as identified from orthologous gene analysis of bulk RNAseq and ATACseq datasets. Highlighted in bold are the genes which we knocked out in this study. g The 100 genes whose expression changes allow for the quantitative measurement of progression of D. discoideum from vegetative through slug to fruiting body stages are displayed in this heatmap pseudotime analysis. Expression of srfA, hdaD, ammr1, and smcl1 are also included in this heatmap. Ribosomal gene expression plays an outsized role in determining pseudotime and these genes are marked. h Representative UMAP graphs display the expression levels of srfA, hdaD, ammr1, smcl1, and hspH2 from single cell RNAseq analysis