Fig. 6. Cells defective in parental histone transfer show defects in gene transcription and ERV silencing.

(A and B) Cluster analysis of differentially expressed genes between WT and POLA1-2A (A) and MCM2-2A (B) mutant mouse ES cells by RNA-seq. Results from two independent repeats (rep 1 and rep 2) were shown. FPKM, fragments per kilobase of transcript per million mapped reads. (C) Venn diagram of up-regulated (top) and down-regulated (bottom) genes between POLA1-2A and MCM2-2A mutant mouse ES cells. (D and E) Changes in the transcription of transposable elements (TEs) in POLA1-2A (D) and MCM2-2A (E) relative to WT mouse ES cells. Histograms show the distributions of the log₂ fold change (LFC) of repeat element expression in each mutant relative to WT cells. Orange, transcription of repetitive elements (Repbase with RNA-seq; POLA1-2A n = 2; MCM2-2A n = 2). Blue, transcription of Ensembl genes. (F) Expression analysis of repetitive elements in WT, POLA1-2A, and MCM2-2A mouse ES cells by quantitative PCR. MMERGLN-int (ERV1), IAPEz-int (ERVK), and MERVL-int (ERVL) representing different families of ERVs were tested. Data were plotted as means ± SEM from at least three independent repeats. **P < 0.01 and ***P < 0.001. (G and H) Changes in the enrichment of H3K9me3 in POLA1-2A (G) and MCM2-2A (H) relative to WT mouse ES cells. Histograms show the distributions of the LFC of H3K9me3 density in POLA1-2A and MCM2-2A mutants relative to WT cells. (I) A model for the role of POLA1 in parental histone transfer.