Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites

Abstract

The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs and correlate with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the roles of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligandregulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. T he liver plays a central role in the control of whole-body lipid homeostasis, and hepatic lipid metabolism is continuously adjusted to fit the needs of the organism. This adaptation requires major adjustments in the hepatic metabolic gene program, including a strong upregulation of lipogenic gene expression in the fed state, whereas in the fasting state, the expression of genes involved in fatty acid oxidation as well as ketogenesis and hepatic glucose production is highly induced. Class II nuclear receptors (NRs), i.e., NRs forming heterodimers with retinoid X receptor (RXR), play a key role in coordinating these changes. They include the liver X receptor (LXR) (29, 57) and peroxisome proliferatoractivated receptor (PPAR) (32, 34, 41) families as well as farnesoid X receptor (FXR) (44, 55, 88), pregnane X receptor (PXR) (5, 33), vitamin D receptor (VDR) (43), constitutive androstane receptor (CAR) (3, 9, 23), and retinoic acid receptors (RARs) (13).The LXR family consists of the two subtypes, LXR␣ (NR1H3) and LXR␤ (NR1H2), both of which form obligate heterodimers with RXR. LXR-RXR heterodimers are reported to bind to LXR response elements (LXREs) that consist of a direct repeat of the core sequence 5=-AGGTCA-3= spaced by 4 nucleotides (DR4) (2,72,76,79,92). LXRs are activated by oxidized cholesterol derivatives and play an important role in the regulation of cholesterol homeostasis in the liver. Thus, pharmacological activation of LXR leads to the induction of several genes implicated in reverse cholesterol transport and mobilization of cholesterol, such as the ATP binding cassette (ABC) transporter genes Abca1, Abcg1, Abcg5, and Abcg8 and the apolipoprotein E gene (ApoE) (12,31,37,60,63,84). Furthermore, a recent genomewide study of LXR in human hepatoma cells showed that LXR also downregulates expression of the cholesterologenic genes for lanosterol 14␣-demethylase (Cyp51A1) and squalene synthase (Fdst1) (89). Moreover, LXR activation induces triglyceride synthesis partly through induction of the lipogenic transcription factors sterol regulatory element-binding protein 1c (SREBP-1c) (42,61,95) and carbohydrate response element-binding protein (ChREBP) (8) but also by direct activation of genes encoding lipogenic enzymes such as fatty acid synthase (Fasn), stearoyl coenzyme A (CoA) desaturase (Scd1), ...

Peroxisome Proliferator-Activated Receptor γ and C/EBPα Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading

“…Alternatively, C/EBP␣ and other cooperating factors are able to relax the sequence specificity so much that PPAR␥ can interact with nonconsensus sequences, e.g., direct repeat half sites. Consistent with this, previous work from our group indicated that both PPAR␣ and liver X receptor can associate directly with sequences that have relatively little resemblance to their consensus sequences (67).…”

Novel Mechanism of Positive versus Negative Regulation by Thyroid Hormone Receptor β1 (TRβ1) Identified by Genome-wide Profiling of Binding Sites in Mouse Liver

“…Peaks were assigned to different genomic regions of associated target genes as described under "Results." RXR ChIP peak (33) and DNase hypersensitivity peak (available through the mouse ENCODE project) overlap were determined using custom scripts. For correlation of gene expression changes with differential peaks, we used the microarray data from Ad-TR␤1-PTU versus Ad-TR␤1-T3.…”

“…To evaluate whether the heterodimer is the predominant active form in vivo, we used data from a RXR ChIP-seq experiment from mouse liver that was previously done using an RXR␣ antibody (33). Importantly, the major heterodimer partner for TR in the liver is the RXR␣ isoform (34).…”

Deubiquitylase Inhibition Reveals Liver X Receptor-independent Transcriptional Regulation of the E3 Ubiquitin Ligase IDOL and Lipoprotein Uptake

“…ChIP Sequencing Analysis-Data analysis was performed using bowtie and HOMER (29) on previously published ChIP experiments: GSE50944 (30), GSE35262 (31), and GSE28319 (32). The sequencing experiment was normalized to a total of 10 7 uniquely mapped tags and visualized by preparing custom tracks for the UCSC Genome Browser.…”