Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs

Abstract

Background While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for long non-coding (lnc)RNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection. Results Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNA transcripts were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to TCPOBOP a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3). Conclusions Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and disease.

Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

“…One example is the conservation between strains of the sex-biased expression of Bcl6 and Cux2, two GH-regulated transcriptional repressors (TFs) [71,80] that play a critical role in enhancing the sex-bias of many genes in mouse liver [40,41,79]. We also identified 78 strain-shared sex-biased lncRNAs, which may play regulatory roles in the chromatin-bound fraction either in cis or in trans [18,81,82]. Four of these 78 lncRNAs have been implicated in negative regulation of sex-biased protein-coding genes of the opposite sex bias and inverse hypophysectomy response class (lnc630, lnc2937, lnc7423, lnc9000; Sheet B in S1 Table) [17].…”

“…Underlying regulatory mechanisms are best studied in the liver, where there is extensive transcriptomic and regulatory sex bias in fish [4,5], rats [6,7], mice [8][9][10] and humans [11,12]. In mouse liver, hundreds of genes are expressed in a sex-dependent manner, including protein-coding genes [13], miRNAs [14,15] and lncRNA genes [16][17][18]. Phenotypically, these sex differences in expression contribute to sex differences in chemical sensing and metabolism [19][20][21], response to injury [22,23], and susceptibility to disease [24][25][26][27].…”

Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

“…One example is the conservation between strains of the sex-biased expression of Bcl6 and Cux2, two GH-regulated transcriptional repressors (TFs) [71,79] that play a critical role in enhancing the sexbias of many genes in mouse liver [40,41,78]. We also identified 78 strain-shared sex-biased lncRNAs, which may play regulatory roles in the chromatin-bound fraction, either in cis or in trans [18,80,81]. Four of these lncRNAs have been implicated in negative regulation of sex-biased protein-coding genes of the opposite sex bias and inverse hypophysectomy response class (lnc630, lnc2937, lnc7423, lnc9000; Table S1B) [17].…”

“…Underlying regulatory mechanisms are best studied in the liver, where there is extensive transcriptomic and regulatory sex bias in fish [4,5], rats [6,7], mice [8][9][10] and humans [11,12]. In mouse liver, hundreds of genes are expressed in a sex-dependent manner, including protein-coding genes [13], miRNAs [14,15] and lncRNA genes [16][17][18]. Phenotypically, these sex differences in expression contribute to sex differences in chemical sensing and metabolism [19][20][21], response to injury [22,23], and susceptibility to disease [24][25][26][27].…”

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

“…These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects on both protein-coding genes and lncRNAs.Synopsis: Single nucleus RNA-seq analysis elucidated the cell type-specificity and zonation of the sex-biased murine liver transcriptome, including thousands of long non-coding RNAs. Xenobiotic exposure induced widespread dysregulation, including both gain and loss of sex-biased gene expression and changes in zonation.[ [33][34][35]. Many such lncRNAs have nuclear regulatory functions [36] and are tightly bound to liver chromatin [35].…”