Regulation of Hepatic Long Non-coding RNAs by PXR and CAR Agonists in Mouse Liver.

Altered expression of lncRNAs by environmental chemicals modulates the expression of xenobiotic biotransformation related genes and may serve as therapeutic targets and novel biomarkers of exposure. The pregnane X receptor (PXR/NR1I2) is a critical xenobiotic-sensing nuclear receptor that regulates the expression of many drug-processing genes, and it has similar target gene profiles and DNA binding motifs with another xenobiotic-sensing nuclear receptor, namely constitutive andronstrane receptor (CAR/Nr1i3). To test our hypothesis that lncRNAs are regulated by PXR in concert with protein-coding genes (PCGs) and to compare the PXR-targeted lncRNAs with CAR-targeted lncRNAs, RNA-Seq was performed from livers of adult male C57BL/6 mice treated with corn oil, the PXR agonist PCN, or the CAR agonist TCPOBOP. Among 125,680 known lncRNAs, 3,843 were expressed in liver and 193 were differentially regulated by PXR (among which 40% were also regulated by CAR). The majority of PXR- or CAR-regulated lncRNAs were mapped to the introns and 3'-UTRs of PCGs as well as intergenic regions. Combining the RNA-Seq data with a published PXR ChIP-Seq dataset (Cui et al., 2010b), we identified 774 expressed lncRNAs with direct PXR-DNA binding sites, and 26.8% of differentially expressed lncRNAs had changes in PXR-DNA binding following PCN exposure. De novo motif analysis identified co-localization of PXR with LRH-1, which regulates bile acid synthesis, following PCN exposure. There was limited overlap of PXR binding with an epigenetic mark for transcriptional activation (histone-H3K4-di-methylation, H3K4me2), but no overlap with epigenetic marks for transcriptional silencing (H3K27me3 and DNA methylation). Among differentially expressed lncRNAs, 264 were in proximity of PCGs, and the lncRNA-PCG pairs displayed a high co-regulatory pattern by PXR and CAR activation. This study was among the first to demonstrate that lncRNAs are regulated by PXR and CAR activation and that they may be important regulators of PCGs involved xenobiotic metabolism.