Exploiting genomics and natural genetic variation to decode macrophage enhancers

Romanoski, Casey E.; Link, Verena M.; Heinz, Sven; Glass, Christopher K.

doi:10.1016/j.it.2015.07.006

Cited by 31 publications

(42 citation statements)

References 128 publications

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“…C/EBPb has been shown to interact with the SWI/SNF nucleosome-remodeling complex, protein arginine N-methyltransferase-4 (66), which may potentially affect histone methylation patterns. Moreover, global changes in macrophage enhancer regions on H3K4 methylation marks partly depends on C/EBPs, as demonstrated by global nuclear run-on coupled to deep sequencing analysis (67,68). These studies indicate a close association of H3 methylation changes and C/EBPb binding, which may also apply on miR-155 and miR-146a promoters.…”

Section: Discussionmentioning

confidence: 69%

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages

Doxaki

Kampranis

Eliopoulos

et al. 2015

The Journal of Immunology

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Endotoxin tolerance occurs to protect the organism from hyperactivation of innate immune responses, primarily mediated by macrophages. Regulation of endotoxin tolerance occurs at multiple levels of cell responses and requires significant changes in gene expression. In the process of macrophage activation, induced expression of microRNA (miR)-155 and miR-146a contributes to the regulation of the inflammatory response and endotoxin tolerance. In this article, we demonstrate that expression of both miRNAs is coordinately regulated during endotoxin tolerance by a complex mechanism that involves monoallelic interchromosomal association, alterations in histone methyl marks, and transcription factor binding. Upon activation of naive macrophages, Histone3 was trimethylated at lysine4 and NFκBp65 was bound on both miR-155 and miR-146a gene loci. However, at the stage of endotoxin tolerance, both miR gene loci were occupied by C/EBPβ, NFκBp50, and the repressive Histone3 marks trimethylation of K9 of H3. DNA fluorescence in situ hybridization experiments revealed monoallelic interchromosomal colocalization of miR-155 and miR-146a gene loci at the stage of endotoxin tolerance, whereas RNA-DNA-fluorescence in situ hybridization experiments showed that the colocalized alleles were silenced, suggesting a common repression mechanism. Genetic ablation of Akt1, which is known to abrogate endotoxin tolerance, abolished induction of loci colocalization and C/EBPβ binding, further supporting that this mechanism occurs specifically in endotoxin tolerance. Overall, this study demonstrates that two miRNAs are coordinately regulated via gene colocalization at the three-dimensional chromatin space, same transcriptional machinery, and similar Histone3 methylation profile, contributing to the development of endotoxin tolerance.

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Section: Discussionmentioning

confidence: 69%

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages

Doxaki

Kampranis

Eliopoulos

et al. 2015

The Journal of Immunology

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“…This twofold activity, which reflects polarization of MF phenotypes along the spectrum of M1 to M0 to M2 states, may contribute to the complexity in NRAMP1 activation, by analogy with different profiles of enhancer activation reported in Th1 vs. Th2 lymphocytes [20], even though mechanisms that differentiate Th cell subsets are not governed by combinations of lineage- and stimulus-dependent TFs such as those described in MFs [22,196]. In turn, complex regulation of NRAMP1 expression may partly explain how SNPs may be associated with susceptibility to infections and/or autoimmune diseases in different human populations [111,197,198,199,200].…”

Section: Discussionmentioning

confidence: 99%

Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes

Cellier

2017

Biology

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NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3′ inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3′ CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.

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“…Perhaps most important is the confirmation that S1 and U1 participate in the regulation of the Vdr gene by 1,25(OH) 2 D 3 and PKA activators, respectively, in the mouse in vivo, and by inference that S3 mediates atRA activity in the bone in vivo as well. This confirmation is important in view of the fact that studies are emerging to suggest that the altered environment of many primary cells placed in culture can impact the epigenome and alter sites of regulation (50). Whether these hormone-regulated enhancers contribute to the basal expression of the Vdr gene in bone cells in vivo is unknown given the problems associated with the preparation and analysis of recombinant activity in mice carrying different transgenes with varied copy numbers and with different sites of integration.…”

Section: Discussionmentioning

confidence: 99%

Mechanisms of Enhancer-mediated Hormonal Control of Vitamin D Receptor Gene Expression in Target Cells

Lee

Meyer

Benkusky

et al. 2015

Journal of Biological Chemistry

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Background: Expression of the vitamin D receptor (VDR) is regulated by hormones in a tissue-specific manner. Results: Enhancers potentially involved in the regulation of VDR expression were characterized in mouse tissues in vivo. Conclusion: Regulation of VDR expression is mediated by tissue-specific enhancers. Significance: Defining potential regulatory regions allows us to predict VDR expression in target tissues.The biological actions of 1,25-dihydroxyvitamin D 3 (1,25 (OH) 2 D 3 ) are mediated by the vitamin D receptor (VDR), whose expression in bone cells is regulated positively by 1,25(OH) 2 D 3 , retinoic acid, and parathyroid hormone through both intergenic and intronic enhancers. In this report, we used ChIP-sequencing analysis to confirm the presence of these Vdr gene enhancers in mesenchyme-derived bone cells and to describe the epigenetic histone landscape that spans the Vdr locus. Using bacterial artificial chromosome-minigene stable cell lines, CRISPR/Cas9 enhancer-deleted daughter cell lines, transient transfection/ mutagenesis analyses, and transgenic mice, we confirmed the functionality of these bone cell enhancers in vivo as well as in vitro. We also identified VDR-binding sites across the Vdr gene locus in kidney and intestine using ChIP-sequencing analysis, revealing that only one of the bone cell-type enhancers bound VDR in kidney tissue, and none were occupied by the VDR in the intestine, consistent with weak or absent regulation by the 1,25(OH) 2 D 3 hormone in these tissues, respectively. However, a number of additional sites of VDR binding unique to either kidney or intestine were present further upstream of the Vdr gene, suggesting the potential for alternative regulatory loci. Importantly, virtually all of these regions retained histone signatures consistent with those of enhancers and exhibited unique DNase I hypersensitivity profiles that reflected the potential for chromatin access. These studies define mechanisms associated with hormonal regulation of the Vdr and hint at the differential nature of VDR binding activity at the Vdr gene in different primary target tissues in vivo. The vitamin D receptor (VDR)2 is a member of the nuclear receptor family of genes that mediates the biological activities of 1,25-dihydroxyvitamin D 3 (1,25(OH) 2 D 3 ) in target cells (1)(2)(3)(4). Based upon detection of the VDR protein by immunological methods, the VDR gene is expressed in a wide variety of cell and tissue types both in vitro and in vivo. These tissue types include the intestine, kidney, skeleton, and parathyroid glands, which all play a role in calcium and phosphorus homeostasis (2,5,6) and additional tissues/cells whose functions are not directly involved in the regulation of mineral metabolism. At these particular sites of VDR expression, which include the skin (7,8), immune cells (9 -11), pancreatic ␤ cells (12-14), reproductive tissues (15)(16)(17), placenta (18,19), and others, numerous roles for the VDR have been identified, all associated with the ability of the VDR to regulate th...

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Exploiting genomics and natural genetic variation to decode macrophage enhancers

Cited by 31 publications

References 128 publications

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages

Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes

Mechanisms of Enhancer-mediated Hormonal Control of Vitamin D Receptor Gene Expression in Target Cells

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