The long noncoding RNA LUCAT1 promotes immune gene expression in human macrophages

Abstract

Abstract Long noncoding RNAs (lncRNA) are transcripts larger than 200 nucleotides that mediate their molecular function in an RNA-dependent manner by regulating gene expression at either the transcriptional or post-transcriptional level. lncRNAs play vital roles in many biological processes; however, their functions in immune cells are largely unexplored. Here we describe the expression, function and the mechanism of action of LUCAT1 (Lung cancer associated transcript 1; SCAL1) in human macrophages. While elevated LUCAT1 expression is observed across many cancers, its cellular function in physiological contexts remains unknown. We show that Toll-like receptor 4 (TLR4) and PMA upregulates LUCAT1 expression in human monocyte-derived macrophages and THP1 cells through ERK1/2 signaling. Using 3’-RACE, long-range PCR and RNA FISH, we demonstrate that the LUCAT1 gene transcribes an abundant, 2562-nucleotides long nuclear-localized RNA. Transient perturbation of the nuclear LUCAT1 using antisense oligonucleotides followed by RNA sequencing and protein assays revealed that LUCAT1 promotes the expression of cytokines and chemokines (CSF3, IL24 and CXCL5), transcription factors (NR4A1 and NR4A3), matrix metalloproteinases (MMP1, MMP3 and MMP19) and others in human macrophages. Using siRNA-mediated knockdown of LUCAT1-interacting nuclear proteins, we show that RBMX contributes to the molecular function of LUCAT1, whereas SFPQ controls the biogenesis of the mature LUCAT1. Further, the nuclear LUCAT1 is chromatin-associated, and acts at the level of gene transcription. Collectively, in this study we have uncovered the function of LUCAT1 in macrophages, underscoring the critical roles of lncRNAs in the immune system.