Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Schöne, Stefanie; Bothe, Melissa; Einfeldt, Edda; Borschiwer, Marina; Benner, Philipp; Vingron, Martin; Thomas‐Chollier, Morgane; Meijsing, Sebastiaan H.

doi:10.1371/journal.pgen.1007793

Cited by 32 publications

(26 citation statements)

References 52 publications

(97 reference statements)

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“…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%

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: Methodsmentioning

confidence: 99%

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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“…Here, the precise nucleotide sequence in a GBS is proposed to function as a shaping ligand that specifies GR's transcriptional activity. X-ray crystallography of GR DBD dimers bound to different GBSs showed that conformation of the lever arm in the DBD appeared to be influenced by the DNA sequence (24, 119). Furthermore, the addition of a single GR-binding site was sufficient to convert a gene, which was normally not regulated by GR, into a target gene, such as IL-1 β and IL1R2 in U2OS cells (120).…”

Section: Introductionmentioning

confidence: 99%

Fighting the Fire: Mechanisms of Inflammatory Gene Regulation by the Glucocorticoid Receptor

et al. 2019

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For many decades, glucocorticoids have been widely used as the gold standard treatment for inflammatory conditions. Unfortunately, their clinical use is limited by severe adverse effects such as insulin resistance, cardiometabolic diseases, muscle and skin atrophies, osteoporosis, and depression. Glucocorticoids exert their effects by binding to the Glucocorticoid Receptor (GR), a ligand-activated transcription factor which both positively, and negatively regulates gene expression. Extensive research during the past several years has uncovered novel mechanisms by which the GR activates and represses its target genes. Genome-wide studies and mouse models have provided valuable insight into the molecular mechanisms of inflammatory gene regulation by GR. This review focusses on newly identified target genes and GR co-regulators that are important for its anti-inflammatory effects in innate immune cells, as well as mutations within the GR itself that shed light on its transcriptional activity. This research progress will hopefully serve as the basis for the development of safer immune suppressants with reduced side effect profiles.

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“…RNA-seq data for U2OS-GR cells was generated as previously described ( 32 ), except that cells were treated with 1 μM dexamethasone for 24 h in addition to the 4-h treatment.…”

Section: Methodsmentioning

confidence: 99%

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements

et al. 2019

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The glucocorticoid receptor (GR), a hormone-activated transcription factor, binds to a myriad of genomic binding sites yet seems to regulate a much smaller number of genes. Genome-wide analysis of GR binding and gene regulation has shown that the likelihood of GR-dependent regulation increases with decreased distance of its binding to the transcriptional start site of a gene. To test if we can adopt this knowledge to expand the repertoire of GR target genes, we used CRISPR/Cas-mediated homology-directed repair to add a single GR-binding site directly upstream of the transcriptional start site of each of four genes. To our surprise, we found that the addition of a single GR-binding site can be enough to convert a gene into a GR target. The gain of GR-dependent regulation was observed for two of four genes analyzed and coincided with acquired GR binding at the introduced binding site. However, the gene-specific gain of GR-dependent regulation could not be explained by obvious differences in chromatin accessibility between converted genes and their non-converted counterparts. Furthermore, by introducing GR-binding sequences with different nucleotide compositions, we show that activation can be facilitated by distinct sequences without obvious differences in activity between the GR-binding sequence variants we tested. The approach to use genome engineering to build genomic response elements facilitates the generation of cell lines with tailored repertoires of GR-responsive genes and a framework to test and refine our understanding of the cis-regulatory logic of gene regulation by testing if engineered response elements behave as predicted.

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Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Cited by 32 publications

References 52 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

Fighting the Fire: Mechanisms of Inflammatory Gene Regulation by the Glucocorticoid Receptor

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements

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