MOESM9 of SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation

Additional file 9: Figure S9. Upregulated genes in SMYD5 knockdown cells associated with LTR/ERV elements and decreased H4K20me3. Loss of SMYD5-dependent silencing of LTR/ERV elements influences the expression of nearby genes. (A) Number of differentially expressed (DE) genes between shLuc and shSmyd5 ES cells (fold-change >1.5, p value <0.05). (B) Expression of upregulated genes between shLuc and shSmyd5 ES cells (p = 5.528e−13) (log2 RPKM). (C) Annotation of LTR/ERV elements nearby DE genes in shLuc and shSmyd5 ES using HOMER software [69]. (D) Fold-change expression of LTR/ERV elements at DE genes (A-C) relative to total mRNA in shSmyd5 ES cells relative to shLuc ES cells. (E) Density of H4K20me3 marks nearby LTR/ERV element and within 10 kb of TSS of DE genes. (F) Mouse gene atlas expression analysis evaluated using Network2Canvas [66] demonstrates that lineage and ES cell genes are misexpressed in shSmyd5 ES cells. Each node (square) represents a gene list (shLuc vs shSmyd5 DE genes bound by SMYD5 and containing LTR/LINE element) associated with a gene-set library (mouse gene atlas). The brightness (white) of each node is determined by its p value.