Fig. 6

Loss of H3.3 remodels transcriptional landscape in Tetrahymena. A Volcano plot representation of genes differentially expressed in H3.3 knockout cells in comparison with the wildtype Tetrahymena cells. Each dot represents a single gene. Genes with FDR ≤ 0.05 were considered significant. Significant differential genes are shown as red dots with labels indicating the gene name. A legend is provided. NS: non-significant. B Bar plot showing the RNA-seq expression levels of selected genes in H3.3 KO cells. C Bar graphs showing RT-qPCR results to examine the differential expression of selected genes in H3.3 KO cells. The experiments were performed in biological triplicates, and p-values were calculated using the student’s t-test (∗∗∗p ≤ 0.001, ∗∗p ≤ 0.01, ∗p ≤ 0.05, n.s.: non-significant). Error bars represent standard error of mean (SEM). D Metagene plot showing the input normalized H3.3 ChIP-seq density over differentially expressed genes in H3.3 KO cells in comparison with unaffected genes (left). Venn diagram represents the overlap of significantly upregulated genes in H3.3 KO cells with H3.3 ChIP targets (right). P-value was calculated using the hypergeometric test. E GO enrichment analysis related to biological processes for differentially expressed genes in H3.3 KO cells. F Proposed model for H3 (H3.3)–H4 nuclear transport and chromatin assembly in Tetrahymena. The roles of Nrp1-Asf1 in H3/H4 transport and CAF1 in RD chromatin assembly appear conserved in Tetrahymena, whereas RI deposition, and identity of its cognate chaperone, requires further investigation