Atlas of pathogen-sensitive myeloid lncRNA networks in humans (SMyLR catalog) [RNA-seq]

Long noncoding RNAs (lncRNAs) play crucial roles in eukaryotic biology, yet their functions in the immune system are not fully understood. This study presents a comprehensive resource on the regulation, pathway dependencies, subcellular localizations, and protein interactomes of lncRNAs in immune cells exposed to pathogens. We developed GRADR, a methodology combining gradient profiling and RNA-bound proteome analysis, to map interactomes for all expressed RNAs in a single experiment. Using GRADR and targeted CRISPR multiomics, we identified a network of lncRNAs, including LINC01215, AC022816, and LINC01268 (ROCKI), that influence immunity, mainly through interactions with splicing factors. Our data are compiled into SMyLR, a web interface providing access to our lncRNA regulation and interactome atlas. This resource is expected to significantly advance research into RNA regulation in immunity. Overall design: To determine lncRNAs involved in anti-pathogen immunity and their pathway dependencies, human type II pneumocytes, alveolar macrophages and blood-derived macrophages were treated with microbial Toll-like-receptor (TLR)-ligands or Interferon-alpha (IFNa), as well as with TLR- and IFNa-signaling inhibitors. RNA was isolated and subjected to RNA-seq analysis. The transcripts LINC01268 (ROCKI), AC010980.1, LINC00158, LINC01215 and AC022816.1, identified as immune-inducible lncRNAs, depending on the TLR-NFkB pathway, were silenced in THP1 cells by CRISPR interference, followed by RNA-seq analysis to determine their roles in macrophage immunity. To narrow the subcellular sites of action of lncRNAs, RNA was isolated from cytplasmic and nulcear fractions of LPS-stimulated macrophages and subjected to RNA-seq analysis.