1
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Datta RR, Rister J. The power of the (imperfect) palindrome: Sequence-specific roles of palindromic motifs in gene regulation. Bioessays 2022; 44:e2100191. [PMID: 35195290 PMCID: PMC8957550 DOI: 10.1002/bies.202100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/22/2022]
Abstract
In human languages, a palindrome reads the same forward as backward (e.g., 'madam'). In regulatory DNA, a palindrome is an inverted sequence repeat that allows a transcription factor to bind as a homodimer or as a heterodimer with another type of transcription factor. Regulatory palindromes are typically imperfect, that is, the repeated sequences differ in at least one base pair, but the functional significance of this asymmetry remains poorly understood. Here, we review the use of imperfect palindromes in Drosophila photoreceptor differentiation and mammalian steroid receptor signaling. Moreover, we discuss mechanistic explanations for the predominance of imperfect palindromes over perfect palindromes in these two gene regulatory contexts. Lastly, we propose to elucidate whether specific imperfectly palindromic variants have specific regulatory functions in steroid receptor signaling and whether such variants can help predict transcriptional outcomes as well as the response of individual patients to drug treatments.
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Affiliation(s)
- Rhea R Datta
- Department of Biology, Hamilton College, Clinton, New York, USA
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
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2
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Liu Z, Fei B, Xie L, Liu J, Chen X, Zhu W, Lv L, Ma W, Gao Z, Hou J, She W. Glucocorticoids protect HEI-OC1 cells from tunicamycin-induced cell damage via inhibiting endoplasmic reticulum stress. Open Life Sci 2021; 16:695-702. [PMID: 34250248 PMCID: PMC8253451 DOI: 10.1515/biol-2021-0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/20/2021] [Accepted: 03/24/2021] [Indexed: 11/18/2022] Open
Abstract
Background To analyze mechanisms of action of glucocorticoid treatment for endoplasmic reticulum stress (ERS) in sensorineural hearing loss (SNHL), we aimed to evaluate the expression and activation status of the protein kinase RNA-like ER kinase (PERK)–C/EBP homologous protein (CHOP) pathway, which is the major pathway in the ERS. Methods In the present study, we established an in vitro ERS model using tunicamycin-treated hair-cell-like HEI-OC1 cells. The effect of dexamethasone on proliferation inhibition, apoptosis, and ATF4–CHOP pathway in HEI-OC1 cells was examined by CCK-8 assay, flow cytometry, western blotting, and reverse transcription PCR, respectively. Results In HEI-OC1 cells, dexamethasone was shown to significantly reduce the tunicamycin-induced expression of ATF4 and CHOP in the context of sustained viability and proliferation, a therapeutic effect that was reversible by co-treatment with a glucocorticoid antagonist. Conclusion Dexamethasone can protect hair-cell-like HEI-OC1 cells from ERS damage, which may be one of the mechanisms of action for GCs in SNHL treatment.
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Affiliation(s)
- Zhibiao Liu
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, Nanjing, China
| | - Bing Fei
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Huai’an Hospital of Xuzhou Medical University, 62 South Huaihai Road, Huai’an 223002, China
| | - Lisheng Xie
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
| | - Jin Liu
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Xiaorui Chen
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Wenyan Zhu
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, Nanjing, China
| | - Lingyun Lv
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, Nanjing, China
| | - Wei Ma
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
| | - Ziwen Gao
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
| | - Jie Hou
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline, Nanjing, China
| | - Wandong She
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing 210008, China
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline, Nanjing, China
- Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
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3
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Syed AP, Greulich F, Ansari SA, Uhlenhaut NH. Anti-inflammatory glucocorticoid action: genomic insights and emerging concepts. Curr Opin Pharmacol 2020; 53:35-44. [DOI: 10.1016/j.coph.2020.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
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4
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Lancaster BR, McGhee JD. How affinity of the ELT-2 GATA factor binding to cis-acting regulatory sites controls Caenorhabditis elegans intestinal gene transcription. Development 2020; 147:dev190330. [PMID: 32586978 PMCID: PMC7390640 DOI: 10.1242/dev.190330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
We define a quantitative relationship between the affinity with which the intestine-specific GATA factor ELT-2 binds to cis-acting regulatory motifs and the resulting transcription of asp-1, a target gene representative of genes involved in Caenorhabditis elegans intestine differentiation. By establishing an experimental system that allows unknown parameters (e.g. the influence of chromatin) to effectively cancel out, we show that levels of asp-1 transcripts increase monotonically with increasing binding affinity of ELT-2 to variant promoter TGATAA sites. The shape of the response curve reveals that the product of the unbound ELT-2 concentration in vivo [i.e. (ELT-2free) or ELT-2 'activity'] and the largest ELT-XXTGATAAXX association constant (Kmax) lies between five and ten. We suggest that this (unitless) product [Kmax×(ELT-2free) or the equivalent product for any other transcription factor] provides an important quantitative descriptor of transcription-factor/regulatory-motif interaction in development, evolution and genetic disease. A more complicated model than simple binding affinity is necessary to explain the fact that ELT-2 appears to discriminate in vivo against equal-affinity binding sites that contain AGATAA instead of TGATAA.
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Affiliation(s)
- Brett R Lancaster
- Department of Biochemistry and Molecular Biology, University of Calgary, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Calgary, Alberta T2N 4N1, Canada
| | - James D McGhee
- Department of Biochemistry and Molecular Biology, University of Calgary, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Calgary, Alberta T2N 4N1, Canada
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5
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Tungtur S, Schwingen KM, Riepe JJ, Weeramange CJ, Swint-Kruse L. Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors. Protein Sci 2019; 28:1806-1818. [PMID: 31351028 DOI: 10.1002/pro.3695] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022]
Abstract
To bridge biological and biochemical disciplines, the relationship between in vitro protein biochemical function and in vivo activity must be established. Such studies can (a) help determine whether properties measured in simple, dilute solutions extrapolate to the complex in vivo conditions and (b) illuminate cryptic biological factors that are new avenues for study. We have explored the in vivo-in vitro relationship for chimeras built from LacI/GalR transcription regulators. In prior studies of individual chimeras, amino acid changes that altered in vitro DNA binding affinity exhibited correlated changes in in vivo transcription repression. However, discrepancies arose when the two datasets were compared to each other: Although their DNA binding domains were identical and their in vitro binding affinities spanned the same range, their in vivo repression ranges differed by >50-fold. Here, we determined that the presence of endogenous ligand for one chimera further exacerbated the offset, but that different abilities to simultaneously bind and "loop" two DNA operators resolves the discrepancy. Indeed, results suggest that the lac operon can be looped by even weakly interacting repressor dimers. For looping-competent repressors, we measured in vitro binding to the secondary operator. Surprisingly, this was largely insensitive to amino acid changes in the repressor protein, which reflects altered specificity; this supports the emerging view that the locations of specificity determining positions can be unique to each protein homolog. In aggregate, this work illustrates how a comparative approach can enrich understanding of the in vivo-in vitro relationship and suggest unexpected avenues for future study.
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Affiliation(s)
- Sudheer Tungtur
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Kristen M Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Joshua J Riepe
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Chamitha J Weeramange
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
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6
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Louw A. GR Dimerization and the Impact of GR Dimerization on GR Protein Stability and Half-Life. Front Immunol 2019; 10:1693. [PMID: 31379877 PMCID: PMC6653659 DOI: 10.3389/fimmu.2019.01693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/14/2022] Open
Abstract
Pharmacologically, glucocorticoids, which mediate their effects via the glucocorticoid receptor (GR), are a most effective therapy for inflammatory diseases despite the fact that chronic use causes side-effects and acquired GC resistance. The design of drugs with fewer side-effects and less potential for the development of resistance is therefore considered crucial for improved therapy. Dimerization of the GR is an integral step in glucocorticoid signaling and has been identified as a possible molecular site to target for drug development of anti-inflammatory drugs with an improved therapeutic index. Most of the current understanding regarding the role of GR dimerization in GC signaling derives for dimerization deficient mutants, although the role of ligands biased toward monomerization has also been described. Even though designing for loss of dimerization has mostly been applied for reduction of side-effect profile, designing for loss of dimerization may also be a fruitful strategy for the development of GC drugs with less potential to develop GC resistance. GC-induced resistance affects up to 30% of users and is due to a reduction in the GR functional pool. Several molecular mechanisms of GC-mediated reductions in GR pool have been described, one of which is the autologous down-regulation of GR density by the ubiquitin-proteasome-system (UPS). Loss of GR dimerization prevents autologous down-regulation of the receptor through modulation of interactions with components of the UPS and post-translational modifications (PTMs), such as phosphorylation, which prime the GR for degradation. Rational design of conformationally biased ligands that select for a monomeric GR conformation, which increases GC sensitivity through improving GR protein stability and increasing half-life, may be a productive avenue to explore. However, potential drawbacks to this approach should be considered as well as the advantages and disadvantages in chronic vs. acute treatment regimes.
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Affiliation(s)
- Ann Louw
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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7
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Thormann V, Glaser LV, Rothkegel MC, Borschiwer M, Bothe M, Fuchs A, Meijsing SH. Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements. Life Sci Alliance 2019; 2:2/2/e201800283. [PMID: 30867223 PMCID: PMC6417287 DOI: 10.26508/lsa.201800283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 01/25/2023] Open
Abstract
This study shows that addition of a single transcription factor binding site can be sufficient to convert a gene into a glucocorticoid receptor target. 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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Affiliation(s)
- Verena Thormann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Laura V Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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8
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9
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Hettich J, Gebhardt JCM. Transcription factor target site search and gene regulation in a background of unspecific binding sites. J Theor Biol 2018; 454:91-101. [PMID: 29870697 PMCID: PMC6103292 DOI: 10.1016/j.jtbi.2018.05.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 11/02/2022]
Abstract
Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is accelerated by TF binding to and sliding along unspecific DNA and that unspecific associations alter the occupation frequency of a gene. However, whether target site search time and occupation frequency can be optimized simultaneously is mostly unclear. We developed a transparent and intuitively accessible state-based formalism to calculate search times to target sites on and occupation frequencies of promoters of arbitrary state structure. Our formalism is based on dissociation rate constants experimentally accessible in live cell experiments. To demonstrate our approach, we consider promoters activated by a single TF, by two coactivators or in the presence of a competitive inhibitor. We find that target site search time and promoter occupancy differentially vary with the unspecific dissociation rate constant. Both parameters can be harmonized by adjusting the specific dissociation rate constant of the TF. However, while measured DNA residence times of various eukaryotic TFs correspond to a fast search time, the occupation frequencies of target sites are generally low. Cells might tolerate low target site occupancies as they enable timely gene regulation in response to a changing environment.
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Affiliation(s)
- J Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - J C M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany.
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10
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Oasa S, Mikuni S, Yamamoto J, Kurosaki T, Yamashita D, Kinjo M. Relationship Between Homodimeric Glucocorticoid Receptor and Transcriptional Regulation Assessed via an In Vitro Fluorescence Correlation Spectroscopy-Microwell System. Sci Rep 2018; 8:7488. [PMID: 29748590 PMCID: PMC5945783 DOI: 10.1038/s41598-018-25393-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid receptor (GR) is a hormone-activated transcription regulatory protein involved in metabolism as well as adrenocortical responses to psychosocial stress. Ligand-activated GR localizes to the nucleus, where GR homodimers regulate gene transcription via direct binding to glucocorticoid response elements (GREs). The role of GR homodimers in transcriptional activation has not yet been elucidated. In this study, we determined the concentration of GR homodimer, and its dissociation constant (Kd), at the single-cell level, by using fluorescence correlation spectroscopy (FCS) combined with a microwell system. Results from dissociation constant analysis and diffusion analysis suggested that GR forms complexes with other proteins as well as homodimers. We determined the relationship between the concentration of GR homodimer and transcriptional activity using a triple-color FCS-microwell system-based fluorescent reporter assay. The binding affinity of GR to GREs was analyzed via fluorescence cross-correlation spectroscopy (FCCS). Our findings indicate that the GR homodimer is essential for activating target gene transcription.
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Affiliation(s)
- Sho Oasa
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Tsumugi Kurosaki
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Daisuke Yamashita
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan.
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11
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Clauß K, Popp AP, Schulze L, Hettich J, Reisser M, Escoter Torres L, Uhlenhaut NH, Gebhardt JCM. DNA residence time is a regulatory factor of transcription repression. Nucleic Acids Res 2017; 45:11121-11130. [PMID: 28977492 PMCID: PMC5737411 DOI: 10.1093/nar/gkx728] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 08/08/2017] [Indexed: 12/21/2022] Open
Abstract
Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains. We characterized the DNA residence times of our repressors in living cells using single molecule tracking. The residence times depended non-linearly on the number of repeat domains and differed by more than a factor of six. The factors provoked a residence time-dependent decrease in transcript level of the glucocorticoid receptor-activated gene SGK1. Down regulation of transcription was due to a lower burst frequency in the presence of long binding repressors and is in accordance with a model of competitive inhibition of endogenous activator binding. Our single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation.
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Affiliation(s)
- Karen Clauß
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Achim P Popp
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Lena Schulze
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Matthias Reisser
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Laura Escoter Torres
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), IDO, Parkring 13, 85748 Garching, Munich, Germany
| | - N Henriette Uhlenhaut
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), IDO, Parkring 13, 85748 Garching, Munich, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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12
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Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH, Nettles KW, Kojetin DJ, Ortlund EA. Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. Nucleic Acids Res 2017; 45:8596-8608. [PMID: 28591827 PMCID: PMC5737878 DOI: 10.1093/nar/gkx509] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/05/2017] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achieve context-specific transcriptional outcomes. The DNA-binding-independent mechanism involves tethering of GR to the pro-inflammatory transcription factor activator protein-1 (AP-1) through protein-protein interactions. This mechanism has served as the predominant model of GR-mediated transrepression of inflammatory genes. However, ChIP-seq data have consistently shown GR to occupy AP-1 response elements (TREs), even in the absence of AP-1. Therefore, the current model is insufficient to explain GR action at these sites. Here, we show that GR regulates a subset of inflammatory genes in a DNA-binding-dependent manner. Using structural biology and biochemical approaches, we show that GR binds directly to TREs via sequence-specific contacts to a GR-binding sequence (GBS) half-site found embedded within the TRE motif. Furthermore, we show that GR-mediated transrepression observed at TRE sites to be DNA-binding-dependent. This represents a paradigm shift in the field, showing that GR uses multiple mechanisms to suppress inflammatory gene expression. This work further expands our understanding of this complex multifaceted transcription factor.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William H Hudson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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13
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Starr TN, Picton LK, Thornton JW. Alternative evolutionary histories in the sequence space of an ancient protein. Nature 2017; 549:409-413. [PMID: 28902834 PMCID: PMC6214350 DOI: 10.1038/nature23902] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022]
Abstract
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution. Here we combine ancestral protein reconstruction with deep mutational scanning to characterize alternative histories in the sequence space around an ancient transcription factor, which evolved a novel biological function through well-characterized mechanisms. We find hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history. We find that if evolution had begun from a different starting point within the network of sequences encoding the ancestral function, outcomes with different genetic and biochemical forms would probably have resulted; this contingency arises from the distribution of functional variants in sequence space and epistasis between residues. Our results illuminate the topology of the vast space of possibilities from which history sampled one path, highlighting how the outcome of evolution depends on a serial chain of compounding chance events.
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Affiliation(s)
- Tyler N Starr
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Lora K Picton
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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14
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de Vera IMS, Zheng J, Novick S, Shang J, Hughes TS, Brust R, Munoz-Tello P, Gardner WJ, Marciano DP, Kong X, Griffin PR, Kojetin DJ. Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA. Structure 2017; 25:1506-1518.e4. [PMID: 28890360 DOI: 10.1016/j.str.2017.07.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 07/28/2017] [Indexed: 11/15/2022]
Abstract
Nuclear receptor (NR) transcription factors bind various coreceptors, small-molecule ligands, DNA response element sequences, and transcriptional coregulator proteins to affect gene transcription. Small-molecule ligands and DNA are known to influence receptor structure, coregulator protein interaction, and function; however, little is known on the mechanism of synergy between ligand and DNA. Using quantitative biochemical, biophysical, and solution structural methods, including 13C-detected nuclear magnetic resonance and hydrogen/deuterium exchange (HDX) mass spectrometry, we show that ligand and DNA cooperatively recruit the intrinsically disordered steroid receptor coactivator-2 (SRC-2/TIF2/GRIP1/NCoA-2) receptor interaction domain to peroxisome proliferator-activated receptor gamma-retinoid X receptor alpha (PPARγ-RXRα) heterodimer and reveal the binding determinants of the complex. Our data reveal a thermodynamic mechanism by which DNA binding propagates a conformational change in PPARγ-RXRα, stabilizes the receptor ligand binding domain dimer interface, and impacts ligand potency and cooperativity in NR coactivator recruitment.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Scott Novick
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Travis S Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - William J Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; TSRI High School Student Summer Internship Program, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - David P Marciano
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Xiangming Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA.
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15
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Weikum ER, Okafor CD, D'Agostino EH, Colucci JK, Ortlund EA. Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner. Mol Pharmacol 2017; 92:12-21. [PMID: 28396564 DOI: 10.1124/mol.117.108506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
The synthetic glucocorticoids (GCs) dexamethasone, mometasone furoate, and triamcinolone acetonide are pharmaceutical mainstays to treat chronic inflammatory diseases. These drugs bind to the glucocorticoid receptor (GR), a ligand-activated transcription factor and member of the nuclear receptor superfamily. The GR is widely recognized as a therapeutic target for its ability to counter proinflammatory signaling. Despite the popularity of GCs in the clinic, long-term use leads to numerous side effects, driving the need for new and improved drugs with less off-target pharmacology. X-ray crystal structures have played an important role in the drug-design process, permitting the characterization of robust structure-function relationships. However, steroid receptor ligand-binding domains (LBDs) are inherently unstable, and their crystallization requires extensive mutagenesis to enhance expression and crystallization. Here, we use an ancestral variant of GR as a tool to generate a high-resolution crystal structure of GR in complex with the potent glucocorticoid triamcinolone acetonide (TA) and a fragment of the small heterodimer partner (SHP). Using structural analysis, molecular dynamics, and biochemistry, we show that TA increases intramolecular contacts within the LBD to drive affinity and enhance stability of the receptor-ligand complex. These data support the emerging theme that ligand-induced receptor conformational dynamics at the mouth of the pocket play a major role in steroid receptor activation. This work also represents the first GR structure in complex with SHP, which has been suggested to play a role in modulating hepatic GR function.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - C Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Emma H D'Agostino
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer K Colucci
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
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16
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Weikum ER, Knuesel MT, Ortlund EA, Yamamoto KR. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol 2017; 18:159-174. [PMID: 28053348 PMCID: PMC6257982 DOI: 10.1038/nrm.2016.152] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity. This structural and mechanistic perspective on GR regulatory specificity is likely to extend to other eukaryotic TRFs.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Matthew T Knuesel
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
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17
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Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Vingron M, Thomas-Chollier M, Meijsing SH. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity. Nat Commun 2016; 7:12621. [PMID: 27581526 PMCID: PMC5025757 DOI: 10.1038/ncomms12621] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.
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Affiliation(s)
- Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, Berlin 14195, Germany
| | - Marcel Jurk
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, Berlin 14195, Germany
| | | | - Iris Dror
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Isabelle Lebars
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institute National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institute National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Petra Imhof
- Institute of Theoretical Physics, Free University Berlin, 14195 Berlin, Germany
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, Berlin 14195, Germany
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, U1024, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, F-75005 Paris, France
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, Berlin 14195, Germany
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18
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De Angelis RW, Maluf NK, Yang Q, Lambert JR, Bain DL. Glucocorticoid Receptor-DNA Dissociation Kinetics Measured in Vitro Reveal Exchange on the Second Time Scale. Biochemistry 2015; 54:5306-14. [PMID: 26267475 DOI: 10.1021/acs.biochem.5b00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The glucocorticoid receptor (GR) is a member of the steroid receptor family of ligand-activated transcription factors. Recent live cell imaging studies have revealed that interactions of GR with chromatin are highly dynamic, with average receptor residence times of only seconds. These findings were surprising because early kinetic studies found that GR-DNA interactions in vitro were much slower, having calculated residence times of minutes to hours. However, these latter analyses were conducted at a time when it was possible to work with only either partially purified holoreceptor or its purified but isolated DNA binding domain. Noting these limitations, we reexamined GR-DNA dissociation kinetics using a highly purified holoreceptor shown to be amenable to rigorous study. We first observe that GR-DNA interactions in vitro are not slow as previously thought but converge with in vivo behavior, having residence times of only seconds to tens of seconds. This rapid exchange is seen at six individual response elements and the multisite MMTV promoter used in live cell imaging. Second, GR dissociation rates are identical for all response elements. Thus, previously observed differences in receptor affinity toward these sequences are not due to differences in off rate but in on rate. Finally, dissociation kinetics are biphasic in character. A minimal kinetic model consistent with the data is that in which DNA-bound GR interconverts between states on a second time scale, with dissociation occurring via a multistep process. We speculate that receptor interconversion in this time frame can be recognized by the coregulatory proteins that interact with GR, leading to unique transcriptional responses.
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Affiliation(s)
- Rolando W De Angelis
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Nasib K Maluf
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Qin Yang
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - James R Lambert
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - David L Bain
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
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19
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Oasa S, Sasaki A, Yamamoto J, Mikuni S, Kinjo M. Homodimerization of glucocorticoid receptor from single cells investigated using fluorescence correlation spectroscopy and microwells. FEBS Lett 2015; 589:2171-8. [PMID: 26183204 DOI: 10.1016/j.febslet.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/01/2015] [Indexed: 11/26/2022]
Abstract
Glucocorticoid receptor α (GR) binds to the promoter regions of target genes as a homodimer and activates its transcriptional process. Though the homodimerization is thought to be the initial and essential process, the dissociation constant for homodimerization of GR remains controversial. To quantify homodimerization of (enhanced green fluorescence protein) EGFP-(glucocorticoid receptor) GR, the particle brightness in lysates from single cell was estimated for the fraction of homodimeric EGFP-GR using fluorescence correlation spectroscopy and microwells. Fitting the data with a bimolecular reaction model, the dissociation constant was determined. Moreover slow-diffusion complex was observed. These results suggest that EGFP-GR forms not only a monomer-dimer equivalent state but also a large-molecular-weight complex.
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Affiliation(s)
- Sho Oasa
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido Univesity, Sapporo 001-0021, Japan
| | - Akira Sasaki
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido Univesity, Sapporo 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido Univesity, Sapporo 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido Univesity, Sapporo 001-0021, Japan.
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20
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Sasse SK, Zuo Z, Kadiyala V, Zhang L, Pufall MA, Jain MK, Phang TL, Stormo GD, Gerber AN. Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem 2015; 290:19756-69. [PMID: 26088140 DOI: 10.1074/jbc.m115.668558] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 01/02/2023] Open
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.
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Affiliation(s)
- 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
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21
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Bain DL, De Angelis RW, Connaghan KD, Yang Q, Degala GD, Lambert JR. Dissecting Steroid Receptor Function by Analytical Ultracentrifugation. Methods Enzymol 2015; 562:363-89. [PMID: 26412661 DOI: 10.1016/bs.mie.2015.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Steroid receptors comprise a family of ligand-activated transcription factors. The members include the androgen receptor (AR), estrogen receptor (ER), glucocorticoid receptor (GR), mineralocorticoid receptor (MR), and progesterone receptor (PR). Each receptor controls distinct sets of genes associated with development, metabolism, and homeostasis. Although a qualitative understanding of how individual receptors mediate gene expression has come into focus, quantitative insight remains less clear. As a step toward delineating the physical mechanisms by which individual receptors activate their target genes, we have carried out a systematic dissection of receptor interaction energetics with their multisite regulatory elements. Analytical ultracentrifugation (AUC) has proved indispensable in these studies, in part by revealing the energetics of receptor self-association and its thermodynamic coupling to DNA binding. Here, we discuss these findings in the context of understanding specificity of receptor-mediated gene control. We first highlight the role of sedimentation velocity and sedimentation equilibrium in addressing receptor assembly state, and present a comparative analysis across the receptor family. We then use these results for understanding how receptors assemble at multisite regulatory elements, and hypothesize how these findings might play a role in receptor-specific gene regulation. Finally, we examine receptor behavior in a cellular context, with a view toward linking our in vitro studies with in vivo function.
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Affiliation(s)
- David L Bain
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
| | - Rolando W De Angelis
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Keith D Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Qin Yang
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory D Degala
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - James R Lambert
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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22
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McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW. Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module. Cell 2015; 159:58-68. [PMID: 25259920 DOI: 10.1016/j.cell.2014.09.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/09/2014] [Accepted: 09/03/2014] [Indexed: 11/29/2022]
Abstract
Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs' DNA selectivity and-with our prior work on the evolution of SR ligand specificity during the same interval-show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.
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Affiliation(s)
- Alesia N McKeown
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Jamie T Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Dave W Anderson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Michael N Murphy
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Joseph W Thornton
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA; Department of Ecology and Evolution and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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23
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Khrapunov S, Warren C, Cheng H, Berko E, Greally JM, Brenowitz M. Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity. Biochemistry 2014; 53:3379-91. [PMID: 24828757 PMCID: PMC4045320 DOI: 10.1021/bi500424z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/08/2014] [Indexed: 02/04/2023]
Abstract
The protein MeCP2 mediates epigenetic regulation by binding methyl-CpG (mCpG) sites on chromatin. MeCP2 consists of six domains of which one, the methyl binding domain (MBD), binds mCpG sites in duplex DNA. We show that solution conditions with physiological or greater salt concentrations or the presence of nonspecific competitor DNA is necessary for the MBD to discriminate mCpG from CpG with high specificity. The specificity for mCpG over CpG is >100-fold under these solution conditions. In contrast, the MBD does not discriminate hydroxymethyl-CpG from CpG. The MBD is unusual among site-specific DNA binding proteins in that (i) specificity is not conferred by the enhanced affinity for the specific site but rather by suppression of its affinity for generic DNA, (ii) its specific binding to mCpG is highly electrostatic, and (iii) it takes up as well as displaces monovalent cations upon DNA binding. The MBD displays an unusually high affinity for single-stranded DNA independent of modification or sequence. In addition, the MBD forms a discrete dimer on DNA via a noncooperative binding pathway. Because the affinity of the second monomer is 1 order of magnitude greater than that of nonspecific binding, the MBD dimer is a unique molecular complex. The significance of these results in the context of neuronal function and development and MeCP2-related developmental disorders such as Rett syndrome is discussed.
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Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Christopher Warren
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Huiyong Cheng
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Esther
R. Berko
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - John M. Greally
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Michael Brenowitz
- Department of Biochemistry and Department of
Genetics, Albert Einstein College of Medicine
of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
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24
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Connaghan KD, Yang Q, Miura MT, Moody AD, Bain DL. Homologous steroid receptors assemble at identical promoter architectures with unique energetics of cooperativity. Proteins 2014; 82:2078-87. [PMID: 24648119 DOI: 10.1002/prot.24563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/05/2014] [Accepted: 03/14/2014] [Indexed: 01/27/2023]
Abstract
Steroid receptors comprise a homologous family of ligand-activated transcription factors. The receptors bind largely identical response elements in vitro, yet regulate distinct gene networks in vivo. This paradox raises the issue of how transcriptional specificity is achieved, particularly if multiple receptor populations are competing for identical sites. Noting that receptor-DNA energetics are a primary force in driving transcriptional activity, differences in interaction energetics among the receptors might underlie receptor-specific transcriptional control. Thermodynamic dissections support this premise-upon assembling at an identical promoter architecture, individual receptors exhibit vast differences in cooperative and self-association energetics. More intriguingly, these parameters distribute in a way that mirrors the evolutionary divergence of the steroid receptor family. For example, the closely related progesterone and glucocorticoid receptors (PR and GR) display little or no self-association but strong intersite cooperativity, whereas the more distantly related estrogen receptor (ER-α) shows inverse behavior. These findings suggest that receptors view genomic promoter architectures as a collection of affinity landscapes; receptors select from this landscape via their unique interaction energetics. To test this idea, we analyzed the cooperative binding energetics of the above three receptors using an array of promoters. We find that cooperativity is not only receptor-specific but also highly promoter-specific. Thus PR shows maximal cooperativity at promoters with closely spaced and in phase binding sites. GR cooperativity is maintained over greater distances, is larger energetically, and shows markedly different phase dependency. Finally, ER-α appears incapable of cooperativity regardless of promoter architecture, consistent with its more distant phylogeny.
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Affiliation(s)
- Keith D Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045
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25
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Altonsy MO, Sasse SK, Phang TL, Gerber AN. Context-dependent cooperation between nuclear factor κB (NF-κB) and the glucocorticoid receptor at a TNFAIP3 intronic enhancer: a mechanism to maintain negative feedback control of inflammation. J Biol Chem 2014; 289:8231-9. [PMID: 24500711 DOI: 10.1074/jbc.m113.545178] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
TNF expression is elevated in asthma and other inflammatory airway diseases that are commonly treated with glucocorticoid-based therapies, but the impact of glucocorticoids on negative feedback control of TNF is not well understood. We analyzed the effect of dexamethasone, a potent synthetic glucocorticoid, on TNF-regulated gene expression in cultured airway epithelial cells. Although dexamethasone-mediated activation of the glucocorticoid receptor (GR) potently repressed expression of IL1β, IL8, and several other pro-inflammatory TNF targets, the expression of anti-inflammatory TNF targets such as TNFAIP3 (A20) and NFKBIA was selectively spared or augmented by dexamethasone treatment. Despite divergent effects on gene expression, GR and NF-κB occupancy at the TNFAIP3 locus and GR-repressed targets was similar. A co-occupied intronic TNFAIP3 regulatory element mediated cooperative enhancement of transcription by GR and NF-κB that required the presence of a functional GR binding site (GBS). GBS exchanges between reporters for TNFAIP3 and FKBP5, a canonical GR-induced target, revealed substantial latitude in the GBS sequence requirements for GR/NF-κB cooperation, suggesting that the TNFAIP3 GBS acts primarily as a docking site in this context. Supporting this notion, a selective GR ligand with only weak agonist activity for induction of FKBP5 enabled robust GR/NF-κB cooperative induction of a mutant TNFAIP3 reporter harboring the FKBP5 GBS. Taken together, our data support a model in which the expression of anti-inflammatory targets of TNF is maintained during treatment with glucocorticoids through context-dependent cooperation between GR and NF-κB.
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Affiliation(s)
- Mohammed O Altonsy
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
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Ratman D, Vanden Berghe W, Dejager L, Libert C, Tavernier J, Beck IM, De Bosscher K. How glucocorticoid receptors modulate the activity of other transcription factors: a scope beyond tethering. Mol Cell Endocrinol 2013; 380:41-54. [PMID: 23267834 DOI: 10.1016/j.mce.2012.12.014] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/13/2012] [Accepted: 12/16/2012] [Indexed: 01/11/2023]
Abstract
The activity of the glucocorticoid receptor (GR), a nuclear receptor transcription factor belonging to subclass 3C of the steroid/thyroid hormone receptor superfamily, is typically triggered by glucocorticoid hormones. Apart from driving gene transcription via binding onto glucocorticoid response elements in regulatory regions of particular target genes, GR can also inhibit gene expression via transrepression, a mechanism largely based on protein:protein interactions. Hereby GR can influence the activity of other transcription factors, without contacting DNA itself. GR is known to inhibit the activity of a growing list of immune-regulating transcription factors. Hence, GCs still rule the clinic for treatments of inflammatory disorders, notwithstanding concomitant deleterious side effects. Although patience is a virtue when it comes to deciphering the many mechanisms GR uses to influence various signaling pathways, the current review is testimony of the fact that groundbreaking mechanistic work has been accumulating over the past years and steadily continues to grow.
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Affiliation(s)
- Dariusz Ratman
- Cytokine Receptor Lab, VIB Department of Medical Protein Research, VIB, UGent, Albert Baertsoenkaai 3, B-9000 Gent, Belgium.
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Bain DL, Connaghan KD, Maluf NK, Yang Q, Miura MT, De Angelis RW, Degala GD, Lambert JR. Steroid receptor-DNA interactions: toward a quantitative connection between energetics and transcriptional regulation. Nucleic Acids Res 2013; 42:691-700. [PMID: 24064251 PMCID: PMC3902896 DOI: 10.1093/nar/gkt859] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Steroid receptors comprise an evolutionarily conserved family of transcription factors. Although the qualitative aspects by which individual receptors regulate transcription are well understood, a quantitative perspective is less clear. This is primarily because receptor function is considerably more complex than that of classical regulatory factors such as phage or bacterial repressors. Here we discuss recent advances in placing receptor-specific transcriptional regulation on a more quantitative footing, specifically focusing on the role of macromolecular interaction energetics. We first highlight limitations and challenges associated with traditional approaches for assessing the role of energetics (more specifically, binding affinity) with functional outcomes such as transcriptional activation. We next demonstrate how rigorous in vitro measurements and straightforward interaction models quantitatively relate energetics to transcriptional activity within the cell, and follow by discussing why such an approach is unexpectedly effective in explaining complex functional behavior. Finally, we examine the implications of these findings for considering the unique gene regulatory properties of the individual receptors.
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Affiliation(s)
- David L Bain
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA and Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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28
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De Angelis RW, Yang Q, Miura MT, Bain DL. Dissection of androgen receptor-promoter interactions: steroid receptors partition their interaction energetics in parallel with their phylogenetic divergence. J Mol Biol 2013; 425:4223-35. [PMID: 23917122 DOI: 10.1016/j.jmb.2013.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 01/24/2023]
Abstract
Steroid receptors comprise a homologous family of ligand-activated transcription factors. The members include androgen receptor (AR), estrogen receptor (ER), glucocorticoid receptor (GR), mineralocorticoid receptor (MR), and progesterone receptor (PR). Phylogenetic studies demonstrate that AR, GR, MR, and PR are most closely related, falling into subgroup 3C. ER is more distantly related, falling into subgroup 3A. To determine the quantitative basis by which receptors generate their unique transcriptional responses, we are systematically dissecting the promoter-binding energetics of all receptors under a single "standard state" condition. Here, we examine the self-assembly and promoter-binding energetics of full-length AR and a mutant associated with prostate cancer, T877A. We first demonstrate that both proteins exist only as monomers, showing no evidence of dimerization. Although this result contradicts the traditional understanding that steroid receptors dimerize in the absence of DNA, it is fully consistent with our previous work demonstrating that GR and two PR isoforms either do not dimerize or dimerize only weakly. Moreover, both AR proteins exhibit substantial cooperativity between binding sites, again as seen for GR and PR. In sharp contrast, the more distantly related ER-α dimerizes so strongly that energetics can only be measured indirectly, yet cooperativity is negligible. Thus, homologous receptors partition their promoter-binding energetics quite differently. Moreover, since receptors most closely related by phylogeny partition their energetics similarly, such partitioning appears to be evolutionarily conserved. We speculate that such differences in energetics, coupled with different promoter architectures, serve as the basis for generating receptor-specific promoter occupancy and thus function.
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Affiliation(s)
- Rolando W De Angelis
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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29
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The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol 2013; 20:876-83. [PMID: 23728292 PMCID: PMC3702670 DOI: 10.1038/nsmb.2595] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 04/09/2013] [Indexed: 12/27/2022]
Abstract
Glucocorticoid receptor binds to genomic response elements and regulates gene transcription with cell- and gene-specificity. Within a response element, the precise sequence to which the receptor binds has been implicated in directing its structure and activity. We use NMR chemical shift difference mapping to show that non-specific interactions with particular base positions within the binding sequence, such as those of the “spacer”, affect the conformation of distinct regions of the rat glucocorticoid receptor DNA binding domain. These regions include the DNA-binding surface, the “lever arm” and the dimerization interface, suggesting an allosteric pathway that signals between the DNA binding sequence and the associated dimer partner. Disrupting this path by mutating the dimer interface alters sequence-specific conformations, DNA-binding kinetics and transcriptional activity. Our study demonstrates that glucocorticoid receptor dimer partners collaborate to read DNA shape and to direct sequence specific gene activity.
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30
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Robertson S, Rohwer JM, Hapgood JP, Louw A. Impact of glucocorticoid receptor density on ligand-independent dimerization, cooperative ligand-binding and basal priming of transactivation: a cell culture model. PLoS One 2013; 8:e64831. [PMID: 23717665 PMCID: PMC3661511 DOI: 10.1371/journal.pone.0064831] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/18/2013] [Indexed: 11/26/2022] Open
Abstract
Glucocorticoid receptor (GR) levels vary between tissues and individuals and are altered by physiological and pharmacological effectors. However, the effects and implications of differences in GR concentration have not been fully elucidated. Using three statistically different GR concentrations in transiently transfected COS-1 cells, we demonstrate, using co-immunoprecipitation (CoIP) and fluorescent resonance energy transfer (FRET), that high levels of wild type GR (wtGR), but not of dimerization deficient GR (GRdim), display ligand-independent dimerization. Whole-cell saturation ligand-binding experiments furthermore establish that positive cooperative ligand-binding, with a concomitant increased ligand-binding affinity, is facilitated by ligand-independent dimerization at high concentrations of wtGR, but not GRdim. The down-stream consequences of ligand-independent dimerization at high concentrations of wtGR, but not GRdim, are shown to include basal priming of the system as witnessed by ligand-independent transactivation of both a GRE-containing promoter-reporter and the endogenous glucocorticoid (GC)-responsive gene, GILZ, as well as ligand-independent loading of GR onto the GILZ promoter. Pursuant to the basal priming of the system, addition of ligand results in a significantly greater modulation of transactivation potency than would be expected solely from the increase in ligand-binding affinity. Thus ligand-independent dimerization of the GR at high concentrations primes the system, through ligand-independent DNA loading and transactivation, which together with positive cooperative ligand-binding increases the potency of GR agonists and shifts the bio-character of partial GR agonists. Clearly GR-levels are a major factor in determining the sensitivity to GCs and a critical factor regulating transcriptional programs.
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Affiliation(s)
- Steven Robertson
- Department of Biochemistry, University of Stellenbosch, Matieland, Stellenbosch, Republic of South Africa
| | - Johann M. Rohwer
- Department of Biochemistry, University of Stellenbosch, Matieland, Stellenbosch, Republic of South Africa
| | - Janet P. Hapgood
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, Republic of South Africa
| | - Ann Louw
- Department of Biochemistry, University of Stellenbosch, Matieland, Stellenbosch, Republic of South Africa
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Connaghan KD, Miura MT, Maluf NK, Lambert JR, Bain DL. Analysis of a glucocorticoid-estrogen receptor chimera reveals that dimerization energetics are under ionic control. Biophys Chem 2012; 172:8-17. [PMID: 23333595 DOI: 10.1016/j.bpc.2012.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 12/11/2012] [Accepted: 12/19/2012] [Indexed: 11/28/2022]
Abstract
Steroid receptors assemble at DNA response elements as dimers, resulting in coactivator recruitment and transcriptional activation. Our work has focused on dissecting the energetics associated with these events and quantitatively correlating the results with function. A recent finding is that different receptors dimerize with large differences in energetics. For example, estrogen receptor-α (ER-α) dimerizes with a ΔG=-12.0 kcal/mol under conditions in which the glucocorticoid receptor (GR) dimerizes with a ΔG≤-5.1 kcal/mol. To determine the molecular forces responsible for such differences, we created a GR/ER chimera, replacing the hormone-binding domain (HBD) of GR with that of ER-α. Cellular and biophysical analyses demonstrate that the chimera is functionally active. However, GR/ER dimerization energetics are intermediate between the parent proteins and coupled to a strong ionic linkage. Since the ER-α HBD is the primary contributor to dimerization, we suggest that GR residues constrain an ion-regulated HBD assembly reaction.
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Affiliation(s)
- Keith D Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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