Summary Epithelial cells along the mucosal surface provide the front line of host defense against pathogen infection in the gastrointestinal (GI) tract. These epithelial cells represent an integral component of a highly regulated communication network that can transmit essential signals to cells in the underlying GI mucosa that, in turn, serve as targets of mucosal immune mediators. How intestinal epithelial cells orchestrate GI mucosal defense is still not fully understood. LncRNAs are recently identified long non-coding transcripts that can regulate gene transcription through their interactions with other effect molecules. We have recently identified a panel of lncRNAs that are upregulated in GI epithelial cells following microbial challenge. Specific lncRNAs display a significant suppressive effect on Type I interferon (IFN)-controlled gene transcription in GI epithelial cells. Interestingly, induction of some lncRNAs is controlled by Type I IFN signaling. Given the emerging significance of lncRNAs in regulation of both innate and adaptive immune responses, coupled with the key role of Type I IFN signaling in regulating GI homeostasis, we speculate that lncRNAs may be important regulators in GI physiology and pathophysiology. In this study, we hypothesize that lncRNAs provide negative feedback regulation of Type I IFN signaling through suppression of Type I IFN-controlled gene transcription, consequently contributing to fine-tuning of epithelial cell innate defense against microbial infection. We will use in vitro, ex vivo and in vivo infection models and complementary biochemical, molecular, and morphologic approaches to elucidate the molecular mechanisms by which lncRNAs modulate Type I IFN-mediated gene transcription in GI epithelial cells (Aim 1) and determine the role of lncRNA- mediated feedback regulation of Type I IFN-mediated gene transcription in GI epithelial innate defense (Aim 2). Therefore, this application will explore a novel mechanism for lncRNAs in regulating GI mucosal innate immunity. Elucidating the regulation of key signal pathways in GI epithelial cells by lncRNAs may reveal new insights into the molecular immunology and immunopathology of the GI tract.