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The transcription factor vitamin D receptor (VDR) is the high affinity nuclear target of the biologically active form of vitamin D3 (1,25(OH)2D3). In order to identify pure genomic transcriptional effects of 1,25(OH)2D3, we used VDR cistrome, transcriptome and open chromatin data, obtained from the human monocytic cell line THP-1, for a novel hierarchical analysis applying three bioinformatics approaches. We predicted 75.6% of all early 1,25(OH)2D3-responding (2.5 or 4 h) and 57.4% of the late differentially expressed genes (24 h) to be primary VDR target genes. VDR knockout led to a complete loss of 1,25(OH)2D3–induced genome-wide gene regulation. Thus, there was no indication of any VDR-independent non-genomic actions of 1,25(OH)2D3 modulating its transcriptional response. Among the predicted primary VDR target genes, 47 were coding for transcription factors and thus may mediate secondary 1,25(OH)2D3 responses. CEBPA and ETS1 ChIP-seq data and RNA-seq following CEBPA knockdown were used to validate the predicted regulation of secondary vitamin D target genes by both transcription factors. In conclusion, a directional network containing 47 partly novel primary VDR target transcription factors describes secondary responses in a highly complex vitamin D signaling cascade. The central transcription factor VDR is indispensable for all transcriptome-wide effects of the nuclear hormone.
The molecular basis of vitamin D signaling implies that the metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) of the secosteroid vitamin D3 activates the transcription factor vitamin D receptor (VDR), which in turn modulates the expression of hundreds of primary vitamin D target genes. Since the evolutionary role of nuclear receptors, such as VDR, was the regulation of cellular metabolism, the control of calcium metabolism became the primary function of vitamin D and its receptor. Moreover, the nearly ubiquitous expression of VDR enabled vitamin D to acquire additional physiological functions, such as the support of the innate immune system in its defense against microbes. Monocytes and their differentiated phenotypes, macrophages and dendritic cells, are key cell types of the innate immune system. Vitamin D signaling was most comprehensively investigated in THP-1 cells, which are an established model of human monocytes. This includes the 1,25(OH)2D3-modulated cistromes of VDR, the pioneer transcription factors PU.1 and CEBPA and the chromatin modifier CTCF as well as of the histone markers of promoter and enhancer regions, H3K4me3 and H3K27ac, respectively. These epigenome-wide datasets led to the development of our chromatin model of vitamin D signaling. This review discusses the mechanistic basis of 189 primary vitamin D target genes identified by transcriptome-wide analysis of 1,25(OH)2D3-stimulated THP-1 cells and relates the epigenomic basis of four different regulatory scenarios to the physiological functions of the respective genes.
Die 5 Lipoxygenase (5 LO) ist das Schlüsselenzym in der Synthese von Leukotrienen. Sie wird auf transkriptioneller und posttranskriptioneller Ebene reguliert. Die Differenzierung myeloider Zelllinien mit 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) und transformierendem Wachstumsfaktor beta (TGFbeta) führt zu einer Erhöhung der 5 LO mRNA-, Protein-Bildung und der zellulären Enzymaktivität. Hier wurde gezeigt, dass dabei reife, nicht jedoch prä-mRNA der 5 LO im Zytosol und im Zellkern stark angereichert wird und dass beide Agentien in die mRNA-Prozessierung eigreifen. Obwohl die Bindung von VDR-Retinoid-X-Rezeptor (RXR)-Heterodimeren an Bindungsstellen im 5 LO-Promotor mittels DNAseI-Footprinting und EMSAs nachgewiesen wurde, konnten Reportergene unter der Kontrolle des 5 LO-Promotors in transienten und stabilen Transfektionen durch 1,25(OH)2D3/TGFbeta nicht stimuliert werden. Offensichtlich wird die Induktion der Expression der 5 LO durch 1,25(OH)2D3/TGFbeta durch Elemente außerhalb des Promotors vermittelt. In transienten Transfektionen führte der Einbau der kodierenden Sequenz der 5 LO in Luziferase-Plasmide bei Cotransfektion von VDR/RXR zu einer 5 fachen Induktion der Reportergen-Aktivität durch 1,25(OH)2D3/TGFbeta, was durch zusätzlichen Einbau der letzten vier Introns auf eine 13-fache Erhöhung gesteigert wurde. Der VDR zeigte einen Ligand-unabhängigen Effekt. Diese Reportergen-Effekte waren promotorunabhängig und von der kodierenden Sequenz gesteuert. RT-PCR-Analyse wies auf eine Deletion von Teilen der kodierenden Sequenz im Laufe der mRNA-Prozessierung hin, was durch 1,25(OH)2D3/TGFbeta verhindert wird. Auch Cotransfektion der TGFbeta-Effektoren Smads 3/4 führte in Abhängigkeit von der kodierenden Sequenz und in geringerem Maße von der 3'-UTR und den Introns J M, aber unabhängig vom Promotor, zu einer starken Erhöhung der Reportergenaktivität. Die 5 LO-Expression wird in den untersuchten Zellen vermutlich durch posttranskriptionelle Prozesse (Splicing, mRNA-Reifung) herunterreguliert, während 1,25(OH)2D3/TGFbeta die Expression der 5 LO durch eine Gegenregulation zu erhöhen, an der Komplexe beteiligt sind, die vermutlich Smads, VDR-RXR-Dimere, andere Transkriptionsfaktoren, Coaktivatoren, RNA-Polymerase II und Splicing-Faktoren enthalten. Hyperacetylierung des 5 LO-Promoters durch Inkubation mit mit dem Histondeacetylase-Inhibitor TsA führte zu einer transkriptionellen Aktivierung. Die kodierende Sequenz (und die Introns) wirkt diesem Effekt vermutlich durch die Rekrutierung von HDACs an VDR oder Smads, die direkt oder indirekt an die kodierende Region binden, entgegen.
Human 5-lipoxygenase (5-LO) is the key enzyme of leukotriene biosynthesis, mostly expressed in leukocytes and thus a crucial component of the innate immune system.
In this study, we show that 5-LO, besides its canonical function as an arachidonic acid metabolizing enzyme, is a regulator of gene expression associated with euchromatin. By Crispr-Cas9-mediated 5-LO knockout (KO) in MonoMac6 (MM6) cells and subsequent RNA-Seq analysis, we identified 5-LO regulated genes which could be clustered to immune/defense response, cell adhesion, transcription and growth/developmental processes. Analysis of differentially expressed genes identified cyclooxygenase-2 (COX2, PTGS2) and kynureninase (KYNU) as strongly regulated 5-LO target genes. 5-LO knockout affected MM6 cell adhesion and tryptophan metabolism via inhibition of the degradation of the immunoregulator kynurenine. By subsequent FAIRE-Seq and 5-LO ChIP-Seq analyses, we found an association of 5-LO with euchromatin, with prominent 5-LO binding to promoter regions in actively transcribed genes. By enrichment analysis of the ChIP-Seq results, we identified potential 5-LO interaction partners. Furthermore, 5-LO ChIP-Seq peaks resemble patterns of H3K27ac histone marks, suggesting that 5-LO recruitment mainly takes place at acetylated histones.>
In summary, we demonstrate a noncanonical function of 5-LO as transcriptional regulator in monocytic cells.
Spatial genome organization is tightly controlled by several regulatory mechanisms and is essential for gene expression control. Nuclear receptors are ligand-activated transcription factors that modulate physiological and pathophysiological processes and are primary pharmacological targets. DNA binding of the important loop-forming insulator protein CCCTC-binding factor (CTCF) was modulated by 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). We performed CTCF HiChIP assays to produce the first genome-wide dataset of CTCF long-range interactions in 1,25(OH)2D3-treated cells, and to determine whether dynamic changes of spatial chromatin interactions are essential for fine-tuning of nuclear receptor signaling. We detected changes in 3D chromatin organization upon vitamin D receptor (VDR) activation at 3.1% of all observed CTCF interactions. VDR binding was enriched at both differential loop anchors and within differential loops. Differential loops were observed in several putative functional roles including TAD border formation, promoter-enhancer looping, and establishment of VDR-responsive insulated neighborhoods. Vitamin D target genes were enriched in differential loops and at their anchors. Secondary vitamin D effects related to dynamic chromatin domain changes were linked to location of downstream transcription factors in differential loops. CRISPR interference and loop anchor deletion experiments confirmed the functional relevance of nuclear receptor ligand-induced adjustments of the chromatin 3D structure for gene expression regulation.