Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer–promoter contacts

Thormann, Verena; Rothkegel, Maika C; Schöpflin, Robert; Glaser, Laura V.; Djurić, Petar M.; Li, Na; Chung, Ho‐Ryun; Schwahn, Kevin; Vingron, Martin; Meijsing, Sebastiaan H.

doi:10.1093/nar/gky122

Cited by 17 publications

(9 citation statements)

References 71 publications

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“…For GILZ , each of the GR-occupied peaks in an ∼100 kb window centered on the regulated promoters is also occupied by AR (Figure 6B ). We previously showed that simultaneous deletion of the promoter-proximal peaks and a region downstream of GILZ containing multiple peaks resulted in a virtual loss of GR-dependent regulation ( 27 ). Re-examination of the clonal lines confirmed that the proximal enhancer and distal GR binding sites in the downstream region are required for GR-dependent regulation of GILZ .…”

Section: Resultsmentioning

confidence: 99%

“…For U2OS-GR, the RNA-seq data was from previous studies ( 26 , 27 ), ArrayExpress accession number E-MTAB-6738. U2OS-GR cells were treated for 4h with either 1μM Dex or 0.1% ethanol as vehicle control.…”

Section: Methodsmentioning

confidence: 99%

“…ChIP-seq for GR replicate 2 (1 μM Dex, 1.5 h) and ChIP-seq for AR (5 nM R1881, 4 h) was done as described ( 28 ). ChIP-seq experiments targeting histone marks in U2OS-AR (5 nM R1881 or 0,1% dmso as a vehicle control (4 h) and U2OS-GR18 (1 μM Dex or 0.1% EtOH as vehicle control, 1.5 h) cells were done as described before for H3K27ac ( 27 ). Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit (E7370; NEB) according to the manufacturer's instructions and submitted for paired-end Illumina sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Clonal lines with CRISPR/Cas9-deleted GR-bound regulatory regions near the GILZ gene ( GILZ ΔGBS1-4, ΔGBS A-G ) were from a previous study ( 27 ). To generate single-cell-derived clonal lines lacking an AR-bound region upstream of the AQP3 gene, 1 million U2OS-AR cells were transfected with 1.2 μg each of the PX459-AQP3_214 and PX459-AQP3_216 plasmids using the Amaxa V Kit (Lonza).…”

Section: Methodsmentioning

confidence: 99%

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Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Kulik

Bothe

Kibar

et al. 2021

Nucleic Acids Research

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The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Kulik

Bothe

Kibar

et al. 2021

Nucleic Acids Research

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“…2a), and capable of transitioning to a tetramer 19 , why does it not regulate genes efficiently? One of the greatest challenges in the postgenomic era is to functionally link enhancers to the regulation of a specific target gene 42 . Our data shows that GRdim binds~70% of the sites that wild-type can access, and all are found within preaccessible chromatin (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide binding potential and regulatory activity of the glucocorticoid receptor’s monomeric and dimeric forms

et al. 2021

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A widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies based on recovery of enriched half-site response elements suggest monomeric engagement on DNA. Here, we perform genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding even to open chromatin. We also find that GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids.

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How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids

Strickland¹,

Ansari

Dantoft

et al. 2022

FEBS Letters

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Glucocorticoids (GCs) are widely used therapeutic agents to treat a broad range of inflammatory conditions. Their functional effects are elicited by binding to the glucocorticoid receptor (GR), which regulates transcription of distinct gene networks in response to ligand. However, the mechanisms governing various aspects of undesired side effects versus beneficial immunomodulation upon GR activation remain complex and incompletely understood. In this review, we discuss emerging models of inflammatory gene regulation by GR, highlighting GR's regulatory specificity conferred by context‐dependent changes in chromatin architecture and transcription factor or co‐regulator dynamics. GR controls both gene activation and repression, with the repression mechanism being central to favourable clinical outcomes. We describe current knowledge about 3D genome organisation and its role in spatiotemporal transcriptional control by GR. Looking beyond, we summarise the evidence for dynamics in gene regulation by GR through cooperative convergence of epigenetic modifications, transcription factor crosstalk, molecular condensate formation and chromatin looping. Further characterising these genomic events will reframe our understanding of mechanisms of transcriptional repression by GR.

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Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer–promoter contacts

Cited by 17 publications

References 71 publications

Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Genome-wide binding potential and regulatory activity of the glucocorticoid receptor’s monomeric and dimeric forms

How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids

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