Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver

Abstract

Altered expression of long noncoding RNAs (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 1, 4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPO-BOP). Among 125,680 known lncRNAs, 3843 were expressed in liver, and 193 were differentially regulated by PXR (among which 40% were also regulated by CAR). Most PXR-or CAR-regulated lncRNAs were mapped to the introns and 39-untranslated regions (UTRs) of PCGs, as well as intergenic regions. Combining the RNA-Seq data with a published PXR chromatin immunoprecipitation coupled with high-throughput sequencing; cytochrome P450 (P450; ChIP-Seq) data set, we identified 774 expressed lncRNAs with direct PXR-DNA binding sites, and 26.8% of differentially expressed lncRNAs had changes in PXR-DNA binding after PCN exposure. De novo motif analysis identified colocalization of PXR with liver receptor homolog (LRH-1), which regulates bile acid synthesis after 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 [H3 lysine 27 tri-methylation (H3K27me3) and DNA methylation]. Among differentially expressed lncRNAs, 264 were in proximity of PCGs, and the lncRNA-PCG pairs displayed a high coregulatory 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 in xenobiotic metabolism.

Phycocyanin Improves Reproductive Ability in Obese Female Mice by Restoring Ovary and Oocyte Quality

“…Significantly, PC restored the elevated H3K9me3 levels in oocytes caused by obesity. H3K4me2 is another key regulator of early embryonic development and a marker for transcriptional activation (Dempsey and Cui, 2019), and obesity can affect the expression level of H3K4me2. However, intragastric administration of PC did not improve the level of H3K4me2 in obese mice.…”

Chronic exposure to ambient traffic-related air pollution (TRAP) alters gut microbial abundance and bile acid metabolism in a transgenic rat model of Alzheimer’s disease

“…BAs were extracted from frozen LIC samples (n = 5–6 per group) using a similar method as we described previously [34] , [45] with modifications. Briefly, 75–85 mg of feces were used for each sample, and were vortexed in sterile water (2.5 µl per mg of fecal mass) at 4 °C.…”

Interplay between murine sex-biased gene expression and hepatic zonation revealed by single nucleus RNA sequencing

“…LncRNAs show high tissue and cell type specificity [37,38], consistent with their diverse roles in complex biological systems, including the liver, where they impact disease development [39][40][41] and present therapeutic opportunities [42]. LncRNAs can impact specific liver cell-type populations, for example, the lncRNAs Hottip and Meg3, which respectively activate and inhibit hepatic stellate cell activation [43,44].Expression patterns have been reported based on bulk RNA-seq analysis for more than 15,000 liverexpressed lncRNAs under a variety of conditions, including differences in sex [33][34][35] and foreign chemical exposure [35,[45][46][47], however, the liver cell type specificity of the vast majority of liver-expressed lncRNAs is unknown.Hepatic stresses induced by high fat dietary regimens [48,49] and chemical exposures [50][51][52] are often sexdependent, are modulated by GH signaling [53,54], and are associated with the development of liver diseases [11,55]. Furthermore, many hepatic stresses induce pathologies within the liver lobule in a zonedependent manner [56,57], making it important to determine whether sexually dimorphic genes and functions can be ascribed to specific liver cell types or zonal regions of the liver lobule.…”

“…However, the impact of this zonation on sex-biased gene expression, including lncRNA expression, has not been defined. Moreover, it is unclear whether hepatic zonation itself may differ between the sexes.Here, we characterize the transcriptomes of 32,000 individual nuclei extracted from male and female mouse livers, including livers from males infused with GH continuously for one week, which substantially feminizes hepatic gene expression [31], and livers from mice exposed to the CAR agonist ligand TCPOBOP, which dysregulates hundreds of genes, including many lncRNA genes [45,46]. Our findings establish that sex-biased gene expression in the liver is largely limited to hepatocyte populations, and that many sex-biased transcripts are zonated within the liver lobule, with a subset showing sex-dependent zonation.…”

“…Expression patterns have been reported based on bulk RNA-seq analysis for more than 15,000 liverexpressed lncRNAs under a variety of conditions, including differences in sex [33][34][35] and foreign chemical exposure [35,[45][46][47], however, the liver cell type specificity of the vast majority of liver-expressed lncRNAs is unknown.…”