Figure 6. Effect of CTCF and Rad21 depletion on the KSHV lytic gene transcriptional profile defined by RNA-Seq.

A. Transcriptome of iSLK cells at 24(C) are shown on the y-axis and the KSHV genome position on the x axis. Sites where CTCF or Rad21 knockdown leads to increased transcription compared to control are represented above the x-axis in blue. Regions where CTCF or Rad21 knockdown leads to decreased transcription compared to control are shown below the x-axis in red. Black bars show gene groups where the effects of CTCF and Rad21 differ and blue bars show genes that are CTCF and Rad21 dependent rather than repressed (see text). B. Effect of CTCF depletion on KSHV mRNAs. The effect of CTCF depletion on each annotated KSHV transcript is depicted as the log₂ ratio of its RNA abundance in the absence versus presence of CTCF at 48 h after induction. Transcripts whose levels increase with CTCF knockdown are thus shown above the x-axis and transcripts that decrease in abundance with CTCF knockdown are shown below. C. Effect of Rad21 depletion on KSHV mRNAs. The effect of Rad21 depletion on each annotated KSHV transcript is depicted as the log₂ ratio of its RNA abundance in the absence versus presence of Rad21 at 48 h after induction as described in panel (B) above.