MOESM9 of SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation
2017-02-23T05:00:00Z (GMT) by
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 . (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  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.