Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions

Abstract The glucocorticoid receptor (GR) is a ligand-regulated transcription factor (TF) that controls the tissue- and gene-specific transactivation and transrepression of thousands of target genes. Distinct GR DNA binding sequences with activating or repressive activities have been identified, but how they modulate transcription in opposite ways is not known. We show that GR forms phase-separated condensates that specifically concentrate known co-regulators via their intrinsically disordered regions (IDRs) in vitro. A combination of dynamic, multivalent (between IDRs) and specific, stable interactions (between LxxLL motifs and the GR ligand binding domain) control the degree of recruitment. Importantly, GR DNA-binding directs the selective partitioning of co-regulators within GR condensates such that activating DNAs cause enhanced recruitment of co-activators. Our work shows that condensation controls GR function by modulating co-regulator recruitment and provides a mechanism for the up- and down-regulation of GR target genes controlled by distinct DNA recognition elements.

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Short Linear Motifs In Intrinsically Disordered Regions Modulate HOG Signaling Capacity

10.1101/199653 ◽

2017 ◽

Author(s):

Bob Strome ◽

Ian Hsu ◽

Mitchell Li Cheong Man ◽

Taraneh Zarin ◽

Alex Nguyen Ba ◽

...

Keyword(s):

Signal Transduction ◽

Fluorescent Reporter ◽

Short Linear Motifs ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Large Numbers ◽

Evolutionarily Conserved ◽

Linear Motifs ◽

Functionally Diverse ◽

Disordered Regions

AbstractThe effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements known as short linear motifs (SLiMs). To further examine the role of SLiMs in signal transduction, we used a previously devised bioinformatics method to predict evolutionarily conserved SLiMs within a well-characterized pathway in S. cerevisiae. Using a single cell, reporter-based flow cytometry assay in conjunction with a fluorescent reporter driven by a pathway-specific promoter, we quantitatively assessed pathway output via systematic deletions of individual motifs. We found that, when deleted, 34% (10/29) of predicted SLiMs displayed a significant decrease in pathway output, providing evidence that these motifs play a role in signal transduction. In addition, we show that perturbations of parameters in a previously published stochastic model of HOG signaling could reproduce the quantitative effects of 4 out of 7 mutations in previously unknown SLiMs. Our study suggests that, even in well-characterized pathways, large numbers of functional elements remain undiscovered, and that challenges remain for application of systems biology models to interpret the effects of mutations in signalling pathways.One-sentence SummaryMutations of short conserved elements in disordered regions have quantitative effects on a model signaling pathway.

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Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation

10.1101/2020.11.10.376327 ◽

2020 ◽

Author(s):

Filipp Frank ◽

Xu Liu ◽

Eric A. Ortlund

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Glucocorticoid Receptor ◽

Target Genes ◽

Dna Recognition ◽

Receptor Dimerization ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Recognition Elements

AbstractThe glucocorticoid receptor (GR) is a ligand-regulated transcription factor (TF) that controls the tissue- and gene-specific transactivation and transrepression of thousands of target genes. Distinct GR DNA binding sequences with activating or repressive activities have been identified, but how they modulate transcription in opposite ways is not known. We show that GR forms phase-separated condensates that specifically concentrate known co-regulators via their intrinsically disordered regions (IDRs) in vitro. A combination of dynamic, multivalent (between IDRs) and specific, stable interactions (between LxxLL motifs and the GR ligand binding domain) control the degree of recruitment. Importantly, GR DNA-binding directs the selective partitioning of co-regulators within GR condensates such that activating DNAs cause enhanced recruitment of co-activators. Our work shows that condensation controls GR function by modulating co-regulator recruitment and provides a mechanism for the up- and down-regulation of GR target genes controlled by distinct DNA recognition elements.

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Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2024685118 ◽

2021 ◽

Vol 118 (30) ◽

pp. e2024685118

Author(s):

Filipp Frank ◽

Xu Liu ◽

Eric A. Ortlund

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Glucocorticoid Receptor ◽

Target Genes ◽

Dna Recognition ◽

Receptor Dimerization ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Recognition Elements

The glucocorticoid receptor (GR) is a ligand-regulated transcription factor (TF) that controls the tissue- and gene-specific transactivation and transrepression of thousands of target genes. Distinct GR DNA-binding sequences with activating or repressive activities have been identified, but how they modulate transcription in opposite ways is not known. We show that GR forms phase-separated condensates that specifically concentrate known coregulators via their intrinsically disordered regions (IDRs) in vitro. A combination of dynamic, multivalent (between IDRs) and specific, stable interactions (between LxxLL motifs and the GR ligand-binding domain) control the degree of recruitment. Importantly, GR DNA binding directs the selective partitioning of coregulators within GR condensates such that activating DNAs cause enhanced recruitment of coactivators. Our work shows that condensation controls GR function by modulating coregulator recruitment and provides a mechanism for the up- and down-regulation of GR target genes controlled by distinct DNA recognition elements.

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