NIH Research Festival
LncRNAs have been reported to influence multiple gene regulatory processes. Technological advances in RNA-seq platforms allow increasingly deep sequencing and detection of low-abundance RNA species such as lncRNAs. The annotation of lncRNA databases has also undergone marked improvements lately, equipping investigators with a more accurate catalogue of the lncRNA repertoire. We analysed total RNA-seq data from mouse macrophages under various inflammatory and intervention conditions and examined the relationship between expression of lncRNAs and their putative partner mRNAs. We found that the macrophage expression of lncRNAs is strongly regulated by an inflammatory stimulus. Moreover, the expression of a majority of the detectable lncRNAs was correlated or anti-correlated with the partner mRNA(s), across the different treatment conditions. A log linear model captures this relationship well for most of the lncRNA-mRNA pairs, which was robust to the extent that the expression of a lncRNA could be used to predict the abundance of its partner mRNA. We discovered that this pairwise relationship is maintained even in a new cellular context where the transcriptome is globally altered due to the lack of a transcriptional regulator. These results suggest a previously unappreciated tight coupling of lncRNA and mRNA expression during cellular responses to various micro-environmental perturbations.
Scientific Focus Area: Molecular Biology and Biochemistry
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