Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops

Sarah K Sasse; Zheng Zuo; Vineela Kadiyala; Liyang Zhang; Miles A Pufall; Mukesh K Jain; Tzu L Phang; Gary D Stormo; Anthony N Gerber

doi:10.1074/jbc.M115.668558

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Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops

Journal article

Open access

Peer reviewed

Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops

Sarah K Sasse, Zheng Zuo, Vineela Kadiyala, Liyang Zhang, Miles A Pufall, Mukesh K Jain, Tzu L Phang, Gary D Stormo and Anthony N Gerber

The Journal of biological chemistry, Vol.290(32), pp.19756-19769

08/07/2015

DOI: 10.1074/jbc.M115.668558

PMCID: PMC4528137

PMID: 26088140

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Abstract

Combinatorial gene regulation through feed-forward loops (FFLs) can bestow specificity and temporal control to client gene expression; however, characteristics of binding sites that mediate these effects are not established. We previously showed that the glucocorticoid receptor (GR) and KLF15 form coherent FFLs that cooperatively induce targets such as the amino acid-metabolizing enzymes AASS and PRODH and incoherent FFLs exemplified by repression of MT2A by KLF15. Here, we demonstrate that GR and KLF15 physically interact and identify low affinity GR binding sites within glucocorticoid response elements (GREs) for PRODH and AASS that contribute to combinatorial regulation with KLF15. We used deep sequencing and electrophoretic mobility shift assays to derive in vitro GR binding affinities across sequence space. We applied these data to show that AASS GRE activity correlated (r(2) = 0.73) with predicted GR binding affinities across a 50-fold affinity range in transfection assays; however, the slope of the linear relationship more than doubled when KLF15 was expressed. Whereas activity of the MT2A GRE was even more strongly (r(2) = 0.89) correlated with GR binding site affinity, the slope of the linear relationship was sharply reduced by KLF15, consistent with incoherent FFL logic. Thus, GRE architecture and co-regulator expression together determine the functional parameters that relate GR binding site affinity to hormone-induced transcriptional responses. Utilization of specific affinity response functions and GR binding sites by FFLs may contribute to the diversity of gene expression patterns within GR-regulated transcriptomes.

Epithelial Cells - metabolism

Proline Oxidase - chemistry

Epithelial Cells - drug effects

Humans

Molecular Sequence Data

Receptors, Glucocorticoid - metabolism

Bronchi - drug effects

Dexamethasone - pharmacology

Kruppel-Like Transcription Factors - metabolism

Base Sequence

Bronchi - metabolism

Saccharopine Dehydrogenases - genetics

Transcription, Genetic

Electrophoretic Mobility Shift Assay

Proline Oxidase - metabolism

Epithelial Cells - cytology

Nuclear Proteins - genetics

Binding Sites

Bronchi - cytology

Fibroblasts - metabolism

Cell Line

Promoter Regions, Genetic

Proline Oxidase - genetics

Response Elements

Signal Transduction

Gene Expression Regulation

Nuclear Proteins - metabolism

Nuclear Proteins - chemistry

Kruppel-Like Transcription Factors - chemistry

Animals

Saccharopine Dehydrogenases - chemistry

Saccharopine Dehydrogenases - metabolism

Fibroblasts - drug effects

Receptors, Glucocorticoid - genetics

Protein Binding

Fibroblasts - cytology

High-Throughput Nucleotide Sequencing

Mice

Kruppel-Like Transcription Factors - genetics

Receptors, Glucocorticoid - chemistry

Details

Title: Subtitle: Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops
Creators: Sarah K Sasse - From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
Zheng Zuo - Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108-8510
Vineela Kadiyala - From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
Liyang Zhang - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
Miles A Pufall - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
Mukesh K Jain - Case Cardiovascular Research Institute and Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-7290, and
Tzu L Phang - Department of Medicine, University of Colorado, Denver, Colorado 80045
Gary D Stormo - Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108-8510
Anthony N Gerber - From the Department of Medicine, National Jewish Health, Denver, Colorado 80206, Department of Medicine, University of Colorado, Denver, Colorado 80045 gerbera@njhealth.org
Resource Type: Journal article
Publication Details: The Journal of biological chemistry, Vol.290(32), pp.19756-19769
DOI: 10.1074/jbc.M115.668558
PMID: 26088140
PMCID: PMC4528137
NLM abbreviation: J Biol Chem
ISSN: 0021-9258
eISSN: 1083-351X
Publisher: United States
Grant note: UL1 TR001082 / NCATS NIH HHS P30 CA046934 / NCI NIH HHS R01 HL109557 / NHLBI NIH HHS P30-CA046934 / NCI NIH HHS T32 DK007762 / NIDDK NIH HHS R01HL109557 / NHLBI NIH HHS R01 HG000249 / NHGRI NIH HHS HG000249 / NHGRI NIH HHS
Language: English
Date published: 08/07/2015
Academic Unit: Biochemistry and Molecular Biology
Record Identifier: 9984025257502771

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