FIG. 5.

Loss of LSD1 results in the aberrant expression of 588 genes greater than 1.4-fold. (A) A heat map shows up- and downregulation of genes altered by >1.4-fold, clustered by similarity in expression profile, between Lsd1^Lox/Δ3 and Lsd1^Δ3/Δ3 cells. Experiments were performed in triplicate using mRNA from three individual ES cell clones. (B) Quantitative RT-PCR validation of transcripts upregulated in Lsd1^Δ3/Δ3 cells and unchanged control genes. (C) Quantitative RT-PCR validation of transcripts downregulated in Lsd1^Δ3/Δ3 cells. Values are expressed relative to the level of transcript in Lsd1^Lox/Δ3 for panels B and C. Mean values (n = 3) ± SEM are plotted. (D) Functional annotation clustering of upregulated genes, using DAVID, identifies an enrichment for genes with a muscle-specific function. Gene names and associated gene ontology (GO) terms are listed. A green block indicates a corresponding gene term association positively reported. (E) Upregulated genes were subdivided by their original chromatin state in mouse ES cells. Genes were classified by the presence of either trimethylated histone H3 Lys4 (K4me3), Lys27 (K27me3), both Lys4 and Lys27 (K4me3/K27me3), or neither modification (none). The number of upregulated genes, the number of genes present on the WG-6 v2 array with a particular modification, and the enrichment of genes with one of the four potential chromatin states (P value, calculated using a hypergeometric test) are indicated.