A multiomics framework for high-throughput lncRNA characterization uncovers major immune regulators

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.

长链非编码RNA（long noncoding RNAs，lncRNAs）在真核生物生物学中发挥着关键作用，但其在免疫系统中的功能尚未完全阐明。本研究构建了一套针对病原体刺激下免疫细胞内长链非编码RNA的调控机制、通路依赖性、亚细胞定位以及蛋白质相互作用组的综合资源库。我们开发了GRADR——一种整合梯度谱分析与RNA结合蛋白质组分析的方法——可在单次实验中完成所有表达RNA的相互作用组图谱绘制。借助GRADR与靶向CRISPR多组学技术，我们鉴定出了一系列影响免疫功能的长链非编码RNA调控网络，其中包括LINC01215、AC022816以及LINC01268（ROCKI），这类RNA主要通过与剪接因子相互作用发挥功能。我们将研究数据整合至SMyLR平台——一个可访问本研究长链非编码RNA调控与相互作用组图谱集的Web界面。该资源库有望极大推动免疫领域RNA调控相关研究的发展。