Fusobacterium nucleatum infection modulates the transcriptome and epigenome of colon cancer cells in an oxygen-dependent manner [ChIP-seq]

We studied how Fusobacterium nucleatum infection under hypoxia regulated the epigenome and transcriptome of colon cancer cells. The six datasets that are described in this study are labeled as follows: (a) Normoxia - No Bacteria (NN), (b) Normoxia - infection with Fnn (NF), (c) Normoxia - infection with E. coli (NE), (d) Hypoxia - No Bacteria (HN), (e) Hypoxia - infection with Fnn (HF), and (f) Hypoxia - infection with E. coli (HE). We split HCT116 cells into two sets of flasks and conditioned them to hypoxic and normoxic environments. One set of cells continued to proliferate in normoxia (18% oxygen) while the other half was exposed to hypoxia (1% oxygen) for 24 hours. After the initial exposure to the oxygen environment, the conditioned cells were infected with Fnn for 4 hours in their respective oxygen environments in pre-equilibrated media. Infection with non-invasive E. coli with otherwise identical conditions was used as a control to validate host cell response. The cells were further incubated for 24 hours in their respective oxygen environments with pre-equilibrated media before they were extracted for analysis.