Fig 8. Viral genome sites of LTF occupancy.

(A) HCMV genome-wide view of ChIP-Seq results for tagged UL87 and UL79 LTFs at 72 hpi (MOI of 3) expressed by Towne and TB40/E strains, respectively. UL87 and UL79 LTF ChIP-Seq reads were aligned to Towne (FJ616285.1) and TB40/E (KF297339.1) genomes, respectively. Uniquely mapped sequence reads after removal of PCR duplicates constituted DNA fragments 18–400 bp in length. The pileups of these fragments are displayed in spatial relationship to schematically depicted HCMV genome regions—repeat long, RL; unique long, UL; internal repeat short, IRS; unique short, US; and terminal repeat short, TRS. (B) Pol II and LTF ChIP-Seq results compared to spike-in normalized PRO-Seq-Flavo results for 6-h dTag vs. CTRL treatments of HCMV Towne UL87^HF-infected HFF, which is described in Fig 2. UCSC Genome browser views of aligned PRO-Seq-Flavo reads were scaled to allow comparison of dTag vs. CTRL results. Locations of the LTF-unresponsive UL83 promoter TSR and LTF-responsive UL80.5 and UL82 promoter TSRs are denoted. Pol II and UL87 LTF ChIP-Seq were performed in parallel, and the sequence reads were aligned to Towne genome; UL79 LTF ChIP-Seq reads were aligned to TB40/E genome. (C) Browser views of LTF-responsive asUL49 CTGTTTAA and UL48A TATTATC promoters comparing LTF ChIP-Seq and PRO-Seq-Flavo results, using approaches described in panel B. Gray scale heatmaps of UL79 and UL87 LTF ChIP-Seq fragment quantity vs. length (18–400 bp) better resolve positions of UL79 and UL87 LTF ChIP-Seq peak summits mapped to TB40/E and Towne genomes, respectively. (D) Exploded view of asUS29 and US30 promoters showing LTF occupancy in relation to transcription, using the same datasets and approaches applied in panels B and C. The TATATA is positioned -32 and -34 relative to asUS29 MAXTSS and US30 MAXTSS, respectively. The browser view is scaled to allow viewing of both the small US30 TSR and the large asUS29 TSR.