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Idealab: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome

  • Oct 16, 2013 · 5:30 PM
  • Ahnon's

Come join IdeaLab, the global DIYbio Journal Club. Every other week, we will be discussing in detail a recent paper from the bioscience literature, with online participants from Counter Culture Labs, BioCurious, Genspace, and other DIYbio groups.

This week, our own Benjamin Lack will lead us through the discussion of the following paper:

DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability.


DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers and repressors of PA25 activity. Serendipitously, the screen also identified many novel genes, such as TDP1 and TDP2, regulating normal HPV episome stability. MRN and 9-1-1 complexes emerged as important for PA25-mediated episome destruction and were selected for follow-up studies. Mre11, along with other homologous recombination and dsDNA break repair genes, was among the highly significant PA25 repressors. The Mre11 inhibitor Mirin was found to sensitize HPV episomes to PA25 resulting in a ∼5-fold reduction of the PA25 IC50. A novel assay that couples end-labeling of DNA to Q-PCR showed that PA25 causes strand breaks within HPV DNA, and that Mirin greatly enhances this activity. The 9-1-1 complex member Rad9, a representative PA25 enhancer, was transiently phosphorylated in response to PA25 treatment suggesting that it has a role in detecting and signaling episome damage by PA25 to the cell. These results establish that DNA-targeted compounds enter cells and specifically target the HPV episome. This action leads to the activation of numerous DDR pathways and the massive elimination of episomal DNA from cells. Our findings demonstrate that viral episomes can be targeted for elimination from cells by minor groove binding agents, and implicate DDR pathways as important mediators of this process.

Participants can join online via (, or join us in person at Ahnon's.

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  • Thomas R.

    Was disappointed this discussion never tackled the primary idea of the paper: do DNA binding molecules eliminate viral DNA via a DNA damage-dependent mechanism. The discussion was bogged down in a discussion of technology and stats, and IMHO did a very poor job. The discussion of the paper never made it to the 2nd half of the paper upon which the main conclusions were based. It was a sad effort which raises the question of why bother? It seemed like a weak effort that did nothing but degrade rather than promote science. What gives?

    March 19, 2014

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