The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

Abstract

RXR signaling is predicted to have a major impact in macrophages, but neither the biological consequence nor the genomic basis of its ligand activation is known. Comprehensive genome-wide studies were carried out to map liganded RXR-mediated transcriptional changes, active binding sites, and cistromic interactions in the context of the macrophage genome architecture. The macrophage RXR cistrome has 5200 genomic binding sites, which are not impacted by ligand. Active enhancers are characterized by PU.1 binding, an increase of enhancer RNA, and P300 recruitment. Using these features, 387 liganded RXR-bound enhancers were linked to 226 genes, which predominantly reside in CTCF/cohesin-limited functional domains. These findings were molecularly validated using chromosome conformation capture (3C) and 3C combined with sequencing (3C-seq), and we show that selected long-range enhancers communicate with promoters via stable or RXR-induced loops and that some of the enhancers interact with each other, forming an interchromosomal network. A set of angiogenic genes, including Vegfa, has liganded RXR-controlled enhancers and provides the macrophage with a novel inducible program.

Retinoid X Receptor-selective Signaling in the Regulation of Akt/Protein Kinase B Isoform-specific Expression

“…However, increase in H3K27ac on day 1 of differentiation and its further augmentation in the presence of bexarotene were moderate (Fig. 7C) in line with a previous report (40). Nonetheless, global levels of H3K18ac, H3K27ac, and H3 were relatively constant during the early stage of differentiation and not affected by the addition of bexarotene (Fig.…”

“…Recent genome-wide studies have identified H3K27 acetylation as a transcription start site-preferred mark (44). In addition, it has been shown that H4K5/8 acetylation, but not H3K27 acetylation, increases on putative RXR-bound enhancers upon RXR ligand activation (40). Thus our study provides additional molecular insights into how mark-specific histone acetylation may be related to bexarotene-responsive locus activation and consequently gene transcription.…”

“…4). Apart from activating gene transcription upon ligand induction, the function of RXR in the absence of ligand is also important for establishing chromatin signatures at genomic loci (40,45,46). Thus, our data suggest that RXR knockdown per se would perturb RXR-mediated chromatin modifications at regulatory loci and subsequently affect gene expression, i.e.…”

“…Although RXR␣ null mice die in utero and have myocardial and ocular malformations, RXR␤ and RXR␥ null mutants are viable and appear to be normal (32,42). Although the role of RXR in myogenic differentiation is largely unclear, advances in next-generation sequencing have allowed the mapping of genome-wide RXR␣-binding sites in other experimental systems (23,40,43). Here, we demonstrate that bexarotene enhances myogenic differentiation through the activation of RXR (Figs.…”

Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

“…It has also been strongly implicated that eRNAs and enhancer functions are involved in the regulation of inflammatory transcription networks (22,(34)(35)(36)(37); however, it remains to be solved how, and if at all, SE-associated eRNAs (seRNAs) contribute to the regulatory landscape. Using global nuclear run-on sequencing (GRO-Seq) to map the location and orientation of all active RNA polymerases genome-wide (38), we found eRNAs extensively transcribed within the macrophage SE subset.…”