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SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors.

ABSTRACT: We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening Of Self-transcribed Hormone Inducible response elements coupled to sequencing). The protocol is an adaptation of the STARR-seq method, which allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements. Using the nuclear receptors of thyroid hormone as an example, we show that SOSHI-seq is a suitable complement to ChIP-Seq analysis to identify at genome-wide scale the functional response elements occupied by nuclear receptors in chromatin.

ORGANISM(S): Mus musculus

PROVIDER: GSE298259 | GEO | 2025/07/01

REPOSITORIES: GEO

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Project description:Kolodkin2013 - Nuclear receptor-mediated cortisol signalling network This model is described in the article: Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N. Nat Commun 2013; 4: 1792 Abstract: It is an accepted paradigm that extended stress predisposes an individual to pathophysiology. However, the biological adaptations to minimize this risk are poorly understood. Using a computational model based upon realistic kinetic parameters we are able to reproduce the interaction of the stress hormone cortisol with its two nuclear receptors, the high-affinity glucocorticoid receptor and the low-affinity pregnane X-receptor. We demonstrate that regulatory signals between these two nuclear receptors are necessary to optimize the body's response to stress episodes, attenuating both the magnitude and duration of the biological response. In addition, we predict that the activation of pregnane X-receptor by multiple, low-affinity endobiotic ligands is necessary for the significant pregnane X-receptor-mediated transcriptional response observed following stress episodes. This integration allows responses mediated through both the high and low-affinity nuclear receptors, which we predict is an important strategy to minimize the risk of disease from chronic stress. This model is hosted on BioModels Database and identified by: BIOMD0000000576. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors.

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