Effect of HDAC5 knockdown on gene expression. (A) PCA of RNA-seq data demonstrating a high degree of separation of samples after treatment with HDAC5 shRNA (circled). HDAC5 shRNA-treated and control samples are compared with erythroid stage-specific samples derived from human umbilical cord blood. (B) Heat map of genes that are differentially expressed between control and HDAC5 shRNA-treated samples. (C) Numbers of genes that are differentially expressed between control and HDAC5 shRNA-treated cells. (D) Gene ontology biological process terms overrepresented in genes that are upregulated in HDAC5-knockdown polychromatic erythroblasts. There were no significant GO terms for downregulated genes in polychromatic erythroblasts. The color represents adjusted P-values, and the width of the bar indicates the number of differential genes in the category. (E) GO biological process terms overrepresented in genes that are downregulate (a) or upregulate (b) in HDAC5-knockdown orthochromatic erythroblasts. The color represents adjusted P-values, and the width of the bar indicates the number of differential genes in the category. (F) Correlation between changes in chromatin accessibility at gene promoters and changes in gene expression. Polychromatic (left) and orthochromatic (right) erythroblasts. Differences in gene expression after HDAC5 shRNA treatment are plotted based on regions of changed accessibility. Baso, basophilic erythroblasts; Ortho, orthochromatic erythroblasts; Poly, poly chromatic erythroblasts; Pro, proerythroblasts.