lncRNA expression predicts mRNA abundance.

Long noncoding RNAs (lncRNAs) have been reported to influence multiple gene regulatory processes. Technological advances in RNA-seq platforms allow detection of low-abundance RNA species such as lncRNAs. This study examined the relationship between expression of lncRNAs and their putative partner mRNAs. We analyzed total RNA-seq data from mouse macrophages under various inflammatory and intervention conditions. The macrophage expression of lncRNAs is strongly regulated by an inflammatory stimulus. Moreover, the expression of a majority of lncRNAs was correlated or anti-correlated with the partner mRNA(s), across the different treatment conditions. This relationship was maintained even in cells from a distinct genotype. These results suggest a previously unappreciated tight coupling of lncRNA and mRNA expression during macrophage responses to various microenvironmental perturbations.