Fleming, Joseph DGiresi, Paul GLindahl-Allen, MarianneKrall, Elsa BLieb, Jason DStruhl, Kevin2015-04-012015Fleming, Joseph D, Paul G Giresi, Marianne Lindahl-Allen, Elsa B Krall, Jason D Lieb, and Kevin Struhl. 2015. “STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.” Epigenetics & Chromatin 8 (1): 7. doi:10.1186/1756-8935-8-7. http://dx.doi.org/10.1186/1756-8935-8-7.1756-8935http://nrs.harvard.edu/urn-3:HUL.InstRepos:14351194Background: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors. Results: We show that during the transformation process, nucleosome-depleted regions (defined by formaldehyde-assisted isolation of regulatory elements (FAIRE)) are largely unchanged and that both before and during transformation, STAT3 binds almost exclusively to previously open chromatin regions. Roughly, a third of the transformation-inducible genes require STAT3 for the induction. STAT3 and NF-κB appear to drive the regulation of different gene sets during the transformation process. Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity. Lastly, many STAT3 binding sites are also bound by FOS and the expression of several AP-1 factors is altered during transformation in a STAT3-dependent manner, suggesting that STAT3 may cooperate with AP-1 proteins. Conclusions: These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch. In addition, gene expression changes during transformation, whether driven by pre-existing or induced transcription factors, occur largely through pre-existing nucleosome-depleted regions. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-7) contains supplementary material, which is available to authorized users.en-USMCF-10ATransformationFAIRESTAT3FOSJournal Article2015-04-0110.1186/1756-8935-8-7