Identification of TNF-a-Responsive Promoters and Enhancers in the Intestinal Epithelial Cell Model Caco-2

The Caco-2 cell line is one of themost important in vitromodels for enterocytes, and is used to study drug absorptionanddisease, including inflammatoryboweldiseaseandcancer. Inorder touse themodeloptimal-ly, it is necessary tomap its functional entities. In this study, we have generated genome-widemaps of active transcription start sites (TSSs), and active enhancers in Caco-2 cells with or without tumour necrosis factor (TNF)-a stimulation to mimic an inflammatory state. We found 520 promoters that significantly changed their usage level uponTNF-a stimulation; of these, 52%arenot annotated.A subset of thesehas thepotential to confer change in protein function due to protein domain exclusion. Moreover, we locate 890 transcribed enhancer candidates, where ∼50 % are changing in usage after TNF-a stimulation. These enhancers share motif enrichments with similarly responding gene promoters. As a case example, we characterize an enhan-cer regulating the laminin-5g2-chain (LAMC2) genebynuclear factor (NF)-kBbinding. This report is thefirst topresent comprehensive TSS andenhancermapsoverCaco-2 cells, andhighlightsmanynovel inflammation-specific promoters and enhancers. Key words: alternative promoters; inflammation; non-coding RNAs; transcribed enhancers; transcriptional regulation 1