Extended Data Fig. 3: (Related to Fig. 2). Characterization of host cell Z-RNAs generated during HSV-1 infections in murine cells.

a-i, Coverage tracks for exemplar Z-RNAs showing Z22 RIP (green), input total RNA (orange), REDIportal-annotated or newly identified A → I editing sites (red ticks, top), positions of qPCR primers (red arrows), and a schematic of the putative Z-RNA structure (bottom). Coverage exceeding indicated limits is denoted by thick black caps. Here, Z-RNAs are produced by 3′ extension of host cell mRNA transcription (a-g), including into neighbouring genes (Tmem230 in b or Rab34 in d), or by de novo transcripts generated in the opposite direction from Hmga1 and Anapc4 genes (h, i). j, RNA eluted from Z22 or control IgG antibody pulldowns from WT HSV-1-infected cells (MOI = 2, 8 h post-infection) were examined by qPCR for exemplar Z-RNAs in panels (Fig. 2e–h, Extended Data Fig. 3a–i). Positions of qPCR primers are shown as red arrows in Fig. 2e–h, Extended Data Fig. 3a–i. Data were normalized to Input. k, RNA eluted from anti-FLAG antibody pulldowns from either FLAG-ZBP1 or FLAG-ZBP1 ΔZα mutant MEFs infected with HSV-1 (MOI = 2; 8 h post-infection) were examined by qPCR for exemplar Z-RNAs in panels (Fig. 2e–h, Extended Data Fig. 3a–i). Positions of qPCR primers are shown as red arrows in Fig. 2e–h, Extended Data Fig. 3a–i. Data were normalized to Input. Data are mean ± s.d. (n = 3 biologically independent samples in j, k). Two-tailed unpaired t-test with Welch’s correction (j). One-way ANOVA with Dunnett’s multiple comparisons test (k). *P < 0.05, **P < 0.005, ***P < 0.0005.