34: LincRNA-Cox2 is a long noncoding RNA induced by TLRs that mediates both activation and repression of immune response genes

An inducible program of inflammatory gene expression is central to anti-microbial defenses. Signal-dependent activation of transcription factors, transcriptional co-regulators and chromatin modifying factors collaborate to control this response. Large intervening non-coding RNAs (LincRNAs) are a relatively new class of genes identified as key regulators of distinct cellular functions. LincRNAs are typically 200 to thousands of nucleotides in length. It has been known for many years that a small number of lincRNAs play roles in regulating epigenetic processes such as X chromosome inactivation and imprinting, however their role in innate immunity has not been examined. Toll like receptors sense microbial infection and activate an inducible inflammatory gene expression program, important in host defense. Here we identify lincRNA-Cox2 as a highly inducible non coding RNA that acts as a key regulator of this inflammatory response. LincRNA-Cox2 is transcribed in the opposite orientation to its proximal gene Ptgs2 (Cox2). It is 1.8kb in length and we have identified three splice variants of the transcript. Expression of lincRNA-Cox2 can be induced by ligands such as LPS, Pam3CSK4 and R848 in a MyD88 and NFkB dependent manner. To define the functional role of lincRNA-Cox2 in inflammatory gene expression, we generated macrophage cell lines in which lincRNA-Cox2 expression was silenced by shRNA. We conducted whole transcriptome analysis on macrophages deficient in lincRNA-Cox2 and results show that this lincRNA mediates both the activation and repression of distinct classes of innate immune genes. Knockdown of lincRNA-Cox2 directly resulted in increased basal levels of a number of interferon stimulated genes such as Ccl5 (Rantes) and IP10. Transcriptional repression of target genes is dependent on interactions of lincRNA-Cox2 with heterogeneous nuclear ribonucleoprotein A/B and A2/B1. Collectively, these studies unveil a central role of lincRNA-Cox2 as a broad acting regulatory component of the circuit that controls the TLR-induced inflammatory response.