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Functions of the proteasome on chromatin. Biomolecules 2014; 4:1026-44. [PMID: 25422899 PMCID: PMC4279168 DOI: 10.3390/biom4041026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/11/2014] [Accepted: 11/10/2014] [Indexed: 12/11/2022] Open
Abstract
The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome.
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Mazaira GI, Lagadari M, Erlejman AG, Galigniana MD. The Emerging Role of TPR-Domain Immunophilins in the Mechanism of Action of Steroid Receptors. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- G. I. Mazaira
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Lagadari
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - A. G. Erlejman
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. D. Galigniana
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
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Cato L, Neeb A, Brown M, Cato ACB. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L. NUCLEAR RECEPTOR SIGNALING 2014; 12:e005. [PMID: 25422595 PMCID: PMC4242288 DOI: 10.1621/nrs.12005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/20/2014] [Indexed: 01/23/2023]
Abstract
Molecular chaperones encompass a group of unrelated proteins that facilitate the
correct assembly and disassembly of other macromolecular structures, which they
themselves do not remain a part of. They associate with a large and diverse set
of coregulators termed cochaperones that regulate their function and
specificity. Amongst others, chaperones and cochaperones regulate the activity
of several signaling molecules including steroid receptors, which upon ligand
binding interact with discrete nucleotide sequences within the nucleus to
control the expression of diverse physiological and developmental genes.
Molecular chaperones and cochaperones are typically known to provide the correct
conformation for ligand binding by the steroid receptors. While this
contribution is widely accepted, recent studies have reported that they further
modulate steroid receptor action outside ligand binding. They are thought to
contribute to receptor turnover, transport of the receptor to different
subcellular localizations, recycling of the receptor on chromatin and even
stabilization of the DNA-binding properties of the receptor. In addition to
these combined effects with molecular chaperones, cochaperones are reported to
have additional functions that are independent of molecular chaperones. Some of
these functions also impact on steroid receptor action. Two well-studied
examples are the cochaperones p23 and Bag-1L, which have been identified as
modulators of steroid receptor activity in nuclei. Understanding details of
their regulatory action will provide new therapeutic opportunities of
controlling steroid receptor action independent of the widespread effects of
molecular chaperones.
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Affiliation(s)
- Laura Cato
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Antje Neeb
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Myles Brown
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Andrew C B Cato
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
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Sung MH, Guertin MJ, Baek S, Hager GL. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 2014; 56:275-285. [PMID: 25242143 DOI: 10.1016/j.molcel.2014.08.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/05/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022]
Abstract
Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a timescale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor-binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach.
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Affiliation(s)
- Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Michael J Guertin
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
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Liberman AC, Antunica-Noguerol M, Arzt E. Modulation of the Glucocorticoid Receptor Activity by Post-Translational Modifications. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Ana Clara Liberman
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
| | - María Antunica-Noguerol
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires
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Distinctly different dynamics and kinetics of two steroid receptors at the same response elements in living cells. PLoS One 2014; 9:e105204. [PMID: 25133404 PMCID: PMC4136857 DOI: 10.1371/journal.pone.0105204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 07/22/2014] [Indexed: 01/01/2023] Open
Abstract
Closely related transcription factors (TFs) can bind to the same response elements (REs) with similar affinities and activate transcription. However, it is unknown whether transcription is similarly orchestrated by different TFs bound at the same RE. Here we have compared the recovery half time (t1/2), binding site occupancy and the resulting temporal changes in transcription upon binding of two closely related steroid receptors, the androgen and glucocorticoid receptors (AR and GR), to their common hormone REs (HREs). We show that there are significant differences at all of these levels between AR and GR at the MMTV HRE when activated by their ligands. These data show that two TFs bound at the same RE can have significantly different modes of action that can affect their responses to environmental cues.
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Single-molecule analysis of transcription factor binding at transcription sites in live cells. Nat Commun 2014; 5:4456. [PMID: 25034201 PMCID: PMC4144071 DOI: 10.1038/ncomms5456] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 06/19/2014] [Indexed: 12/22/2022] Open
Abstract
Although numerous live-cell measurements have shown that transcription factors (TFs) bind chromatin transiently, no measurements of transient binding have been reported at the endogenous response elements (REs) where transcription is normally induced. Here we show that at endogenous REs the transcriptionally productive specific binding of two TFs, p53 and the glucocorticoid receptor (GR), is transient. We also find that the transient residence times of GR at endogenous REs are roughly comparable to those at an artificial, multi-copy array of gene regulatory sites, supporting the use of multi-copy arrays for live-cell analysis of transcription. Finally, we find that at any moment only a small fraction of TF molecules are engaged in transcriptionally productive binding at endogenous REs. The small fraction of bound factors provides one explanation for gene bursting and it also indicates that REs may often be unoccupied, resulting in partial responses to transcriptional signals.
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Abstract
The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms.
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Live cell imaging unveils multiple domain requirements for in vivo dimerization of the glucocorticoid receptor. PLoS Biol 2014; 12:e1001813. [PMID: 24642507 PMCID: PMC3958349 DOI: 10.1371/journal.pbio.1001813] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/06/2014] [Indexed: 12/20/2022] Open
Abstract
The glucocorticoid receptor's oligomerization state is revealed to not correlate with its activity; this challenges the current prevailing view that this state defines its transcriptional activity. Glucocorticoids are essential for life, but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses. Glucocorticoid receptor (GR) transcriptional activity and clinical outcome have been linked to its oligomerization state. Although a point mutation within the GR DNA-binding domain (GRdim mutant) has been reported as crucial for receptor dimerization and DNA binding, this assumption has recently been challenged. Here we have analyzed the GR oligomerization state in vivo using the number and brightness assay. Our results suggest a complete, reversible, and DNA-independent ligand-induced model for GR dimerization. We demonstrate that the GRdim forms dimers in vivo whereas adding another mutation in the ligand-binding domain (I634A) severely compromises homodimer formation. Contrary to dogma, no correlation between the GR monomeric/dimeric state and transcriptional activity was observed. Finally, the state of dimerization affected DNA binding only to a subset of GR binding sites. These results have major implications on future searches for therapeutic glucocorticoids with reduced side effects. The powerful anti-inflammatory and immunosuppressive action of glucocorticoids have made them one of the most prescribed drugs worldwide. Unfortunately, acute or chronic treatment may have severe side-effects. Glucocorticoids bind to the glucocorticoid receptor (GR), a ligand-dependent transcription factor. GR regulates gene expression directly by binding to DNA or indirectly by modulating the activity of other transcription factors. It is currently accepted that the direct pathway is mostly responsible for glucocorticoids side-effects and that the oligomerization state of the GR (whether it is a dimer or a monomer) determines which pathway (direct or indirect) will prevail. Hence, scientists have tried to develop “dissociated ligands” able to specifically activate the GR indirect pathway. In the present work, we employed a novel microscopy method named the number and brightness assay, which measures GR oligomerization state inside the living cell. Our results suggest that—contrary to the established view—there is no clear correlation between the oligomerization state of GR and the mechanistic pathway the receptor will follow upon ligand binding. This discovery presents supporting evidence towards the increasing view of the inherent complexity of glucocorticoid action and might impact future approaches towards the design of safer synthetic glucocorticoids.
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60
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Groeneweg FL, van Royen ME, Fenz S, Keizer VIP, Geverts B, Prins J, de Kloet ER, Houtsmuller AB, Schmidt TS, Schaaf MJM. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP. PLoS One 2014; 9:e90532. [PMID: 24632838 PMCID: PMC3954550 DOI: 10.1371/journal.pone.0090532] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 02/02/2014] [Indexed: 02/01/2023] Open
Abstract
Recent advances in live cell imaging have provided a wealth of data on the dynamics of transcription factors. However, a consistent quantitative description of these dynamics, explaining how transcription factors find their target sequences in the vast amount of DNA inside the nucleus, is still lacking. In the present study, we have combined two quantitative imaging methods, single-molecule microscopy and fluorescence recovery after photobleaching, to determine the mobility pattern of the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR), two ligand-activated transcription factors. For dexamethasone-activated GR, both techniques showed that approximately half of the population is freely diffusing, while the remaining population is bound to DNA. Of this DNA-bound population about half the GRs appeared to be bound for short periods of time (∼ 0.7 s) and the other half for longer time periods (∼ 2.3 s). A similar pattern of mobility was seen for the MR activated by aldosterone. Inactive receptors (mutant or antagonist-bound receptors) show a decreased DNA binding frequency and duration, but also a higher mobility for the diffusing population. Likely, very brief (≤ 1 ms) interactions with DNA induced by the agonists underlie this difference in diffusion behavior. Surprisingly, different agonists also induce different mobilities of both receptors, presumably due to differences in ligand-induced conformational changes and receptor complex formation. In summary, our data provide a consistent quantitative model of the dynamics of GR and MR, indicating three types of interactions with DNA, which fit into a model in which frequent low-affinity DNA binding facilitates the search for high-affinity target sequences.
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Affiliation(s)
- Femke L. Groeneweg
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
| | | | - Susanne Fenz
- Physics of Life Processes, Institute of Physics (LION), Leiden University, Leiden, The Netherlands
- Cell & Developmental Biology, Biocenter, Würzburg University, Würzburg, Germany
| | - Veer I. P. Keizer
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Bart Geverts
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Jurrien Prins
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - E. Ron de Kloet
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
| | | | - Thomas S. Schmidt
- Physics of Life Processes, Institute of Physics (LION), Leiden University, Leiden, The Netherlands
| | - Marcel J. M. Schaaf
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
- * E-mail:
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Vandenbunder B, Fourré N, Leray A, Mueller F, Völkel P, Angrand PO, Héliot L. PRC1 components exhibit different binding kinetics in Polycomb bodies. Biol Cell 2014; 106:111-25. [PMID: 24460908 DOI: 10.1111/boc.201300077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/21/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND INFORMATION Polycomb group (PcG) proteins keep the memory of cell identity by maintaining the repression of numerous target genes. They accumulate into nuclear foci called Polycomb bodies, which function in Drosophila cells as silencing compartments where PcG target genes convene. PcG proteins also exert their activities elsewhere in the nucleoplasm. In mammalian cells, the dynamic organisation and function of Polycomb bodies remain to be determined. RESULTS Fluorescently tagged PcG proteins CBXs and their partners BMI1 and RING1 form foci of different sizes and intensities in human U2OS cells. Fluorescence recovery after photobleaching (FRAP) analysis reveals that PcG dynamics outside foci is governed by diffusion as complexes and transient binding. In sharp contrast, recovery curves inside foci are substantially slower and exhibit large variability. The slow binding component amplitudes correlate with the intensities and sizes of these foci, suggesting that foci contained varying numbers of binding sites. CBX4-green fluorescent protein (GFP) foci were more stable than CBX8-GFP foci; yet the presence of CBX4 or CBX8-GFP in the same focus had a minor impact on BMI1 and RING1 recovery kinetics. CONCLUSION We propose that FRAP recovery curves provide information about PcG binding to their target genes outside foci and about PcG spreading onto chromatin inside foci.
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Affiliation(s)
- Bernard Vandenbunder
- Biophotonique Cellulaire Fonctionnelle, Interdisciplinary Research Institute, Université Lille 1 - CNRS USR 3078, Parc de la Haute Borne, Villeneuve d'Ascq, 59658, France
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Grossmann C, Ruhs S, Langenbruch L, Mildenberger S, Strätz N, Schumann K, Gekle M. Nuclear shuttling precedes dimerization in mineralocorticoid receptor signaling. ACTA ACUST UNITED AC 2014; 19:742-51. [PMID: 22726688 DOI: 10.1016/j.chembiol.2012.04.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 04/22/2012] [Accepted: 04/25/2012] [Indexed: 10/28/2022]
Abstract
The mineralocorticoid receptor (MR), a member of the steroid receptor superfamily, regulates water-electrolyte balance and mediates pathophysiological effects in the renocardiovascular system. Previously, it was assumed that after binding aldosterone, the MR dissociates from HSP90, forms homodimers, and then translocates into the nucleus where it acts as a transcription factor (Guiochon-Mantel et al., 1989; Robertson et al., 1993; Savory et al., 2001). We found that, during aldosterone-induced nuclear translocation, MR is bound to HSP90 both in the cytosol and the nucleus. Homodimerization measured by eBRET and FRET takes place when the MR is already predominantly nuclear. In vitro binding of MR to DNA was independent of ligand but could be partially inhibited by geldanamycin. Overall, here we provide insights into classical MR signaling necessary for elucidating the mechanisms of pathophysiological MR effects and MR specificity.
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Affiliation(s)
- Claudia Grossmann
- Julius-Bernstein-Institute of Physiology, University Halle-Wittenberg, Halle/Saale 06112, Germany.
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Co-chaperones of Hsp90 in Plasmodium falciparum and their concerted roles in cellular regulation. Parasitology 2014; 141:1177-91. [PMID: 24560171 DOI: 10.1017/s0031182013002084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Co-chaperones are well-known regulators of heat shock protein 90 (Hsp90). Hsp90 is a molecular chaperone that is essential in the eukaryotes for the folding and activation of numerous proteins involved in important cellular processes such as signal transduction, growth and developmental regulation. Co-chaperones assist Hsp90 in the protein folding process by modulating conformational changes to promote client protein interaction and functional maturation. With the recognition of Plasmodium falciparum Hsp90 (PfHsp90) as a potential antimalarial drug target, there is obvious interest in the study of its co-chaperones in their partnership in regulating cellular processes in malaria parasite. Previous studies on PfHsp90 have identified more than 10 co-chaperones in P. falciparum genome. However, many of them remained annotated as putative proteins as their functionality has not been validated experimentally. So far, only five co-chaperones, PfHop, Pfp23, PfAha1, PfPP5 and PfFKBP35 have been characterized and shown to interact with PfHsp90. This review will summarize current knowledge on the co-chaperones in P. falciparum and discuss their regulatory roles on PfHsp90. As certain eukaryotic co-chaperones have also been implicated in altering the affinity of Hsp90 for its inhibitor, this review will also examine plasmodial co-chaperones' potential influence on approaches towards designing antimalarials targeting PfHsp90.
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Miranda TB, Morris SA, Hager GL. Complex genomic interactions in the dynamic regulation of transcription by the glucocorticoid receptor. Mol Cell Endocrinol 2013; 380:16-24. [PMID: 23499945 PMCID: PMC3724757 DOI: 10.1016/j.mce.2013.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/26/2013] [Accepted: 03/03/2013] [Indexed: 12/13/2022]
Abstract
The glucocorticoid receptor regulates transcriptional output through complex interactions with the genome. These events require continuous remodeling of chromatin, interactions of the glucocorticoid receptor with chaperones and other accessory factors, and recycling of the receptor by the proteasome. Therefore, the cohort of factors expressed in a particular cell type can determine the physiological outcome upon treatment with glucocorticoid hormones. In addition, circadian and ultradian cycling of hormones can also affect GR response. Here we will discuss revision of the classical static model of GR binding to response elements to incorporate recent findings from single cell and genome-wide analyses of GR regulation. We will highlight how these studies have changed our views on the dynamics of GR recruitment and its modulation of gene expression.
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65
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Dickmeis T, Weger BD, Weger M. The circadian clock and glucocorticoids--interactions across many time scales. Mol Cell Endocrinol 2013; 380:2-15. [PMID: 23707790 DOI: 10.1016/j.mce.2013.05.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 12/20/2022]
Abstract
Glucocorticoids are steroid hormones of the adrenal gland that are an integral component of the stress response and regulate many physiological processes, including metabolism and immune response. Their release into the blood is highly dynamic and occurs in about hourly pulses, the amplitude of which is modulated in a daytime dependent fashion. In addition, in many species seasonal changes in basal glucocorticoid levels have been reported. In their target tissues, glucocorticoids bind to cytoplasmic receptors of the nuclear receptor superfamily. Upon binding, these receptors regulate transcription in a highly dynamic fashion, which involves stochastic binding to regulatory DNA elements on a time scale of seconds and heat shock protein mediated receptor-ligand complex recycling within minutes. The glucocorticoid hormone system interacts with another highly dynamic system, the circadian clock. The circadian clock is an endogenous biological timing mechanism that allows organisms to anticipate regular daily changes in their environment. It regulates daily rhythms of glucocorticoid release by a variety of mechanisms, modulates glucocorticoid signaling and is itself influenced by glucocorticoids. Here, we discuss mechanisms, functions and interactions of the circadian and glucocorticoid systems across time scales ranging from seconds (DNA binding by transcriptional regulators) to years (seasonal rhythms).
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Affiliation(s)
- Thomas Dickmeis
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
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Larson DR, Fritzsch C, Sun L, Meng X, Lawrence DS, Singer RH. Direct observation of frequency modulated transcription in single cells using light activation. eLife 2013; 2:e00750. [PMID: 24069527 PMCID: PMC3780543 DOI: 10.7554/elife.00750] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 08/20/2013] [Indexed: 12/21/2022] Open
Abstract
Single-cell analysis has revealed that transcription is dynamic and stochastic, but tools are lacking that can determine the mechanism operating at a single gene. Here we utilize single-molecule observations of RNA in fixed and living cells to develop a single-cell model of steroid-receptor mediated gene activation. We determine that steroids drive mRNA synthesis by frequency modulation of transcription. This digital behavior in single cells gives rise to the well-known analog dose response across the population. To test this model, we developed a light-activation technology to turn on a single steroid-responsive gene and follow dynamic synthesis of RNA from the activated locus. DOI:http://dx.doi.org/10.7554/eLife.00750.001 The process by which a gene is expressed as a protein consists of two stages: transcription, which involves the DNA of the gene being copied into messenger RNA (mRNA); and translation, in which the mRNA is used as a template to assemble amino acids into a protein. Transcription and translation are controlled by many interlinked pathways, which ensures that genes are expressed when and where required. One of these regulatory pathways involves steroid receptors. The binding of a steroid molecule to its receptor causes the receptor to move into the nucleus and interact with a specific gene, triggering transcription of that gene. When measured at the level of the whole organism, this transcriptional response is dose-dependent—the more steroid molecules that are present, the greater the amount of transcription. However, this is not the case in single cells, in which transcription is either activated or not. This ‘on/off’ behaviour is also seen over time: steroid-activated transcription occurs in bursts, separated by periods of inactivity. To unravel the molecular mechanism behind this phenomenon, Larson et al. created a light-activated form of the ligand that activates a specific steroid receptor. Using this molecule, they were able to switch transcription of the gene controlled by that receptor on and off. They then used fluorescent proteins to label the mRNA and protein molecules that were produced as a result. They found that activating the steroid receptor increases the likelihood of transcription occurring inside a cell, but not the duration of individual bursts of transcriptional activity, nor the amount of mRNA produced during each burst. Activation of a steroid receptor seems to control transcription by reducing the length of time each cell spends in the ‘off’ state between bursts. Larson et al. incorporated their findings into a model that also takes into account the natural variability in levels of transcription between cells, and found that this could explain how the digital (on/off) control of transcription at the cellular level leads to analogue, dose-dependent control at the level of a whole organism. These findings should lead to further insights into how transcription is controlled at the molecular level. DOI:http://dx.doi.org/10.7554/eLife.00750.002
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Affiliation(s)
- Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , United States
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Mueller F, Stasevich TJ, Mazza D, McNally JG. Quantifying transcription factor kinetics: at work or at play? Crit Rev Biochem Mol Biol 2013; 48:492-514. [PMID: 24025032 DOI: 10.3109/10409238.2013.833891] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Transcription factors (TFs) interact dynamically in vivo with chromatin binding sites. Here we summarize and compare the four different techniques that are currently used to measure these kinetics in live cells, namely fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single molecule tracking (SMT) and competition ChIP (CC). We highlight the principles underlying each of these approaches as well as their advantages and disadvantages. A comparison of data from each of these techniques raises an important question: do measured transcription kinetics reflect biologically functional interactions at specific sites (i.e. working TFs) or do they reflect non-specific interactions (i.e. playing TFs)? To help resolve this dilemma we discuss five key unresolved biological questions related to the functionality of transient and prolonged binding events at both specific promoter response elements as well as non-specific sites. In support of functionality, we review data suggesting that TF residence times are tightly regulated, and that this regulation modulates transcriptional output at single genes. We argue that in addition to this site-specific regulatory role, TF residence times also determine the fraction of promoter targets occupied within a cell thereby impacting the functional status of cellular gene networks. Thus, TF residence times are key parameters that could influence transcription in multiple ways.
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Affiliation(s)
- Florian Mueller
- Institut Pasteur, Computational Imaging and Modeling Unit, CNRS , Paris , France
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68
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Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet 2013; 14:572-84. [PMID: 23835438 DOI: 10.1038/nrg3484] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcriptional regulation is achieved through combinatorial interactions between regulatory elements in the human genome and a vast range of factors that modulate the recruitment and activity of RNA polymerase. Experimental approaches for studying transcription in vivo now extend from single-molecule techniques to genome-wide measurements. Parallel to these developments is the need for testable quantitative and predictive models for understanding gene regulation. These conceptual models must also provide insight into the dynamics of transcription and the variability that is observed at the single-cell level. In this Review, we discuss recent results on transcriptional regulation and also the models those results engender. We show how a non-equilibrium description informs our view of transcription by explicitly considering time- and energy-dependence at the molecular level.
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69
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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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70
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Trebble PJ, Woolven JM, Saunders KA, Simpson KD, Farrow SN, Matthews LC, Ray DW. A ligand-specific kinetic switch regulates glucocorticoid receptor trafficking and function. J Cell Sci 2013; 126:3159-69. [PMID: 23687373 DOI: 10.1242/jcs.124784] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The ubiquitously expressed glucocorticoid receptor (GR) is a major drug target for inflammatory disease, but issues of specificity and target tissue sensitivity remain. We now identify high potency, non-steroidal GR ligands, GSK47867A and GSK47869A, which induce a novel conformation of the GR ligand-binding domain (LBD) and augment the efficacy of cellular action. Despite their high potency, GSK47867A and GSK47869A both induce surprisingly slow GR nuclear translocation, followed by prolonged nuclear GR retention, and transcriptional activity following washout. We reveal that GSK47867A and GSK47869A specifically alter the GR LBD structure at the HSP90-binding site. The alteration in the HSP90-binding site was accompanied by resistance to HSP90 antagonism, with persisting transactivation seen after geldanamycin treatment. Taken together, our studies reveal a new mechanism governing GR intracellular trafficking regulated by ligand binding that relies on a specific surface charge patch within the LBD. This conformational change permits extended GR action, probably because of altered GR-HSP90 interaction. This chemical series may offer anti-inflammatory drugs with prolonged duration of action due to altered pharmacodynamics rather than altered pharmacokinetics.
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Affiliation(s)
- Peter J Trebble
- Manchester Centre for Nuclear Hormone Research in Disease, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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71
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Robertson S, Hapgood JP, Louw A. Glucocorticoid receptor concentration and the ability to dimerize influence nuclear translocation and distribution. Steroids 2013. [PMID: 23178279 DOI: 10.1016/j.steroids.2012.10.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Glucocorticoid receptor (GR) concentrations and the ability of the GR to dimerize are factors which influence sensitivity to glucocorticoids. Upon glucocorticoid binding, the GR is actively transported into the nucleus, a crucial step in determining GR function. We examined the effects of GR concentration and the ability to dimerize on GR nuclear import, export and nuclear distribution using both live cell microscopy of GFP-tagged GR and immunofluorescence of untagged GR, with both wild type GR (GRwt) and dimerization deficient GR (GRdim). We found that the observed rate of GR nuclear import increases significantly at higher GR concentrations, at saturating concentrations of dexamethasone (10(-6) M) using GFP-tagged GR, while with untagged GR it is only discernable at sub-saturating ligand concentrations (10(-10)-10(-9) M). Loss of dimerization results in a slower observed rate of nuclear import (2.5- to 3.3-fold decrease for GFP-GRdim) as well as a decreased extent of GR nuclear localization (18-27% decrease for untagged GRdim). These results were linked to an increased rate of GR export at low GR concentrations (1.4- to 1.6-fold increase for untagged GR) and where GR dimerization is abrogated (1.5- to 1.7-fold increase for GFP-GRdim). Furthermore, GR dimerization was shown to be required for the appearance of discrete GC-dependent GR nuclear foci, the loss of which may explain the increased rate of GR export for the GRdim. The reduction in the observed rate of nuclear import and increased rate of nuclear export displayed at low GR concentrations and by the GRdim could explain the lowered glucocorticoid response under these conditions.
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Affiliation(s)
- Steven Robertson
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa
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72
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Patwardhan CA, Fauq A, Peterson LB, Miller C, Blagg BSJ, Chadli A. Gedunin inactivates the co-chaperone p23 protein causing cancer cell death by apoptosis. J Biol Chem 2013; 288:7313-25. [PMID: 23355466 DOI: 10.1074/jbc.m112.427328] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pharmacological inhibition of Hsp90 is an exciting option for cancer therapy. The clinical efficacy of Hsp90 inhibitors is, however, less than expected. Binding of the co-chaperone p23 to Hsp90 and induced overexpression of anti-apoptotic proteins Hsp70 and Hsp27 are thought to contribute to this outcome. Herein, we report that the natural product gedunin may provide a new alternative to inactivate the Hsp90 machine. We show that gedunin directly binds to p23 and inactivates it, without overexpression of Hsp27 and relatively modest induction of Hsp70. Using molecular docking and mutational analysis, we mapped the gedunin-binding site on p23. Functional analysis shows that gedunin inhibits the p23 chaperoning activity, blocks its cellular interaction with Hsp90, and interferes with p23-mediated gene regulation. Cell treatment with gedunin leads to cancer cell death by apoptosis through inactivation of p23 and activation of caspase 7, which cleaves p23 at the C terminus. These results provide important insight into the molecular mechanism of action of this promising lead compound.
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Affiliation(s)
- Chaitanya A Patwardhan
- Cancer Research Center, Molecular Chaperones Program, Georgia Regents University, Augusta, Georgia 30912, USA
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73
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Ouyang J, Chen P, Jiang T, Chen Y, Li J. Nuclear HSP90 regulates the glucocorticoid responsiveness of PBMCs in patients with idiopathic nephrotic syndrome. Int Immunopharmacol 2012; 14:334-40. [PMID: 22926076 DOI: 10.1016/j.intimp.2012.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 07/23/2012] [Accepted: 08/13/2012] [Indexed: 12/27/2022]
Abstract
Resistance to glucocorticoid (GC) is a challenge for the treatment of patients with idiopathic nephrotic syndrome (INS). Most of the effects of GC are mediated by the GC receptor (GR). Heat shock protein 90 (HSP90) is an important molecular chaperone for the GR and is supposed to be the key factor in regulating GC effects. In a previous study, we found that both the expression and nuclear distribution of HSP90 were increased in GC resistant INS patients. The aim of this study is to explore how these phenomena contribute to GC resistance in INS patients. Healthy subjects and INS patients with different GC responses were recruited. The total HSP90 expression was determined by reverse transcription-PCR and flow cytometric analysis. Western blot analysis was used to evaluate the expression of nuclear HSP90. Co-immunoprecipitation and electrophoretic mobility gel shift assays were performed to explore the interaction between HSP90 and the GR in the nucleus as well as the DNA-binding activity of GR. We induced the upregulation of the expression of total HSP90 in PBMCs by treatment with interleukin-6 in vitro and found that the nuclear HSP90 level, the DNA-binding activity of the GR and the cell apoptotic responsiveness to GC remained unchanged. Furthermore, an increased nuclear HSP90 was demonstrated mainly by binding to GR in the nucleus, while the DNA-binding activity of the GR dramatically decreased in GC resistant INS patients. The present results suggest that the accumulation of HSP90 in the nucleus potentially hinders DNA-binding activity and transactivation, which may contribute to GC resistance in patients with INS.
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Affiliation(s)
- Juan Ouyang
- Department of Laboratory Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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74
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Stavreva DA, Varticovski L, Hager GL. Complex dynamics of transcription regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:657-66. [PMID: 22484099 PMCID: PMC3371156 DOI: 10.1016/j.bbagrm.2012.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 03/10/2012] [Accepted: 03/15/2012] [Indexed: 01/10/2023]
Abstract
Transcription is a tightly regulated cellular function which can be triggered by endogenous (intrinsic) or exogenous (extrinsic) signals. The development of novel techniques to examine the dynamic behavior of transcription factors and the analysis of transcriptional activity at the single cell level with increased temporal resolution has revealed unexpected elements of stochasticity and dynamics of this process. Emerging research reveals a complex picture, wherein a wide range of time scales and temporal transcription patterns overlap to generate transcriptional programs. The challenge now is to develop a perspective that can guide us to common underlying mechanisms, and consolidate these findings. Here we review the recent literature on temporal dynamics and stochastic gene regulation patterns governed by intrinsic or extrinsic signals, utilizing the glucocorticoid receptor (GR)-mediated transcriptional model to illustrate commonality of these emerging concepts. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Building 41, B507, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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75
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Nguyen PM, Wang D, Wang Y, Li Y, Uchizono JA, Chan WK. p23 co-chaperone protects the aryl hydrocarbon receptor from degradation in mouse and human cell lines. Biochem Pharmacol 2012; 84:838-50. [PMID: 22759865 DOI: 10.1016/j.bcp.2012.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/15/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-sensitive transcription factor which is responsible for most 2,3,7,8-tetrachlorodibenzo-p-dioxin toxicities. Without ligand, the AhR complex is cytoplasmic and contains p23. Our objective was to investigate whether the wild type p23 levels are important for the AhR function. We generated eight p23-specific knockdown stable cell lines via either electroporation or lentiviral infection. Five of these stable cell lines were generated from a mouse hepatoma cell line (Hepa1c1c7) and three were from human hepatoma and cervical cell lines (Hep3B and HeLa). All of them expressed lower AhR protein levels, leading to reduced ligand-induced, DRE-driven downstream activity. The AhR protein levels in p23-specific knockdown stable cells were reversed back to wild type levels after exogenous p23 was introduced. Reduction of the AhR protein levels in these stable cells was caused by a decrease in the AhR message levels and an increase of the AhR protein degradation in the absence of ligand. This ligand-independent degradation of AhR was not reversed by MG132, suggesting that the 26S proteasome was not responsible for the degradation. In addition, MG132 could not protect AhR from the ligand-induced degradation in both mouse and human p23-knockdown stable cells.
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Affiliation(s)
- Phuong Minh Nguyen
- Department of Labour Physiology, Vietnam Military Medical University, Hadong, Hanoi, Viet Nam
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76
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Grøntved L, Hager GL. Impact of chromatin structure on PR signaling: transition from local to global analysis. Mol Cell Endocrinol 2012; 357:30-6. [PMID: 21958695 PMCID: PMC3290724 DOI: 10.1016/j.mce.2011.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 09/02/2011] [Indexed: 01/16/2023]
Abstract
The progesterone receptor (PR) interacts with chromatin in a highly dynamic manner that requires ongoing chromatin remodeling, interaction with chaparones and activity of the proteasome. Here we discuss dynamic interaction of steroid receptor with chromatin, with special attention not only to PR but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS-seq) show that a large fraction of receptor binding events occur at pre-accessible chromatin. Thus factors which generate and maintain accessible chromatin during development, and in fully differentiated tissue, contribute a major fraction of receptor tissue specificity. In addition, chromosome conformation capture techniques suggest that steroid receptors preferentially sequester within distinct nuclear hubs. We will integrate dynamic studies from single cells and genomic studies from cell populations, and discuss how genomic approaches have reshaped our current understanding of mechanisms that control steroid receptor interaction with chromatin.
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Affiliation(s)
- Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892
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77
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Dynamic mechanism for the transcription apparatus orchestrating reliable responses to activators. Sci Rep 2012; 2:422. [PMID: 22639730 PMCID: PMC3360325 DOI: 10.1038/srep00422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/11/2012] [Indexed: 12/02/2022] Open
Abstract
The transcription apparatus (TA) is a huge molecular machine. It detects the time-varying concentrations of transcriptional activators and initiates mRNA transcripts at appropriate rates. Based on the general structural organizations of the TA, we propose how the TA dynamically orchestrates transcriptional responses. The activators rapidly cycle in and out of a clamp-like space temporarily formed between the enhancer and the Mediator, with the concentration of activators encoded as their temporal occupancy rate (RTOR) within the space. The entry of activators into this space induces allostery in the Mediator, resulting in a facilitated circumstance for transcriptional reinitiation. The reinitiation rate is much larger than the cycling rate of activators, thereby RTOR guiding the amount of transcripts. Based on this mechanism, stochastic simulations can qualitatively reproduce and interpret multiple features of gene expression, e.g., transcriptional bursting is not mere noise as traditionally believed, but rather the basis of reliable transcriptional responses.
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78
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Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 2012; 484:251-5. [PMID: 22498630 PMCID: PMC3341663 DOI: 10.1038/nature10985] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 02/23/2012] [Indexed: 12/26/2022]
Abstract
Dynamic access to genetic information is central to organismal development and environmental response. Consequently, genomic processes must be regulated by mechanisms that alter genome function relatively rapidly. Conventional chromatin immunoprecipitation (ChIP) experiments measure transcription factor occupancy, but give no indication of kinetics and are poor predictors of transcription factor function at a given locus. To measure transcription-factor-binding dynamics across the genome, we performed competition ChIP (refs 6, 7) with a sequence-specific Saccharomyces cerevisiae transcription factor, Rap1 (ref. 8). Rap1-binding dynamics and Rap1 occupancy were only weakly correlated (R(2) = 0.14), but binding dynamics were more strongly linked to function than occupancy. Long Rap1 residence was coupled to transcriptional activation, whereas fast binding turnover, which we refer to as 'treadmilling', was linked to low transcriptional output. Thus, DNA-binding events that seem identical by conventional ChIP may have different underlying modes of interaction that lead to opposing functional outcomes. We propose that transcription factor binding turnover is a major point of regulation in determining the functional consequences of transcription factor binding, and is mediated mainly by control of competition between transcription factors and nucleosomes. Our model predicts a clutch-like mechanism that rapidly engages a treadmilling transcription factor into a stable binding state, or vice versa, to modulate transcription factor function.
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Affiliation(s)
- Colin R. Lickwar
- Department of Biology, Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center CB #3280, 408 Fordham Hall University of North Carolina at Chapel Hill Chapel Hill, NC 27599-3280
| | - Florian Mueller
- LRBGE-National Cancer Institute The National Institutes of Health 41 Library Drive Bethesda, MD 20892
- Institut Pasteur Groupe Imagerie et Modélisation Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Sean E. Hanlon
- Department of Biology, Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center CB #3280, 408 Fordham Hall University of North Carolina at Chapel Hill Chapel Hill, NC 27599-3280
| | - James G McNally
- LRBGE-National Cancer Institute The National Institutes of Health 41 Library Drive Bethesda, MD 20892
| | - Jason D. Lieb
- Department of Biology, Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center CB #3280, 408 Fordham Hall University of North Carolina at Chapel Hill Chapel Hill, NC 27599-3280
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79
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Hindley C, Ali F, McDowell G, Cheng K, Jones A, Guillemot F, Philpott A. Post-translational modification of Ngn2 differentially affects transcription of distinct targets to regulate the balance between progenitor maintenance and differentiation. Development 2012; 139:1718-23. [PMID: 22491944 DOI: 10.1242/dev.077552] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Neurogenin 2 (Ngn2) controls neuronal differentiation cell-autonomously by transcriptional activation of targets such as NeuroD, while simultaneously controlling progenitor maintenance non-cell-autonomously by upregulating Delta expression and Notch signalling. Reduction in Cdk-dependent multisite phosphorylation of Ngn2 enhances its promoter binding affinity. This leads specifically to an increase in neuronal differentiation without an apparent increase in progenitor maintenance via Delta-Notch signalling, although the mechanism underlying this imbalance remains unclear. Here we show in Xenopus embryos and mouse P19 cells that the NeuroD promoter is substantially more sensitive to the phosphorylation status of Ngn2 than the Delta promoter, and that this can be attributed to differences in the ease of promoter activation. In addition, we also show that the phosphorylation status of Ngn2 regulates sensitivity to Notch signalling. These observations explain how Ngn2 post-translational modification in response to changes in the cell cycle kinase environment results in enhanced neuronal differentiation upon cell cycle lengthening.
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Affiliation(s)
- Christopher Hindley
- Department of Oncology, University of Cambridge, Hutchison/Medical Research Council (MRC) Research Centre, Cambridge CB2 0XZ,
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80
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Abstract
Regulation of gene transcription is vitally important for the maintenance of normal cellular homeostasis. Failure to correctly regulate gene expression, or to deal with problems that arise during the transcription process, can lead to cellular catastrophe and disease. One of the ways cells cope with the challenges of transcription is by making extensive use of the proteolytic and nonproteolytic activities of the ubiquitin-proteasome system (UPS). Here, we review recent evidence showing deep mechanistic connections between the transcription and ubiquitin-proteasome systems. Our goal is to leave the reader with a sense that just about every step in transcription-from transcription initiation through to export of mRNA from the nucleus-is influenced by the UPS and that all major arms of the system--from the first step in ubiquitin (Ub) conjugation through to the proteasome-are recruited into transcriptional processes to provide regulation, directionality, and deconstructive power.
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Affiliation(s)
- Fuqiang Geng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8240, USA.
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81
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Echtenkamp FJ, Freeman BC. Expanding the cellular molecular chaperone network through the ubiquitous cochaperones. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:668-73. [PMID: 21889547 DOI: 10.1016/j.bbamcr.2011.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 10/17/2022]
Abstract
Cellular environments are highly complex and contain a copious variety of proteins that must operate in unison to achieve homeostasis. To guide and preserve order, multifaceted molecular chaperone networks are present within each cell type. To handle the vast client diversity and regulatory demands, a wide assortment of chaperones are needed. In addition to the classic heat shock proteins, cochaperones with inherent chaperoning abilities (e.g., p23, Hsp40, Cdc37, etc.) are likely used to complete a system. In this review, we focus on the HSP90-associated cochaperones and provide evidence supporting a model in which select cochaperones are used to differentially modulate target proteins, contribute to combinatorial client regulation, and increase the overall reach of a cellular molecular chaperone network. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).
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Affiliation(s)
- Frank J Echtenkamp
- Department of Cell and Development Biology, University of Illinois, Urbana, IL, USA
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82
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Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012; 32:1645-53. [PMID: 22354995 DOI: 10.1128/mcb.06170-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The response to stressful stimuli requires rapid, precise, and dynamic gene expression changes that must be coordinated across the genome. To gain insight into the temporal ordering of genome reorganization, we investigated dynamic relationships between changing nucleosome occupancy, transcription factor binding, and gene expression in Saccharomyces cerevisiae yeast responding to oxidative stress. We applied deep sequencing to nucleosomal DNA at six time points before and after hydrogen peroxide treatment and revealed many distinct dynamic patterns of nucleosome gain and loss. The timing of nucleosome repositioning was not predictive of the dynamics of downstream gene expression change but instead was linked to nucleosome position relative to transcription start sites and specific cis-regulatory elements. We measured genome-wide binding of the stress-activated transcription factor Msn2p over time and found that Msn2p binds different loci with different dynamics. Nucleosome eviction from Msn2p binding sites was common across the genome; however, we show that, contrary to expectation, nucleosome loss occurred after Msn2p binding and in fact required Msn2p. This negates the prevailing model that nucleosomes obscuring Msn2p sites regulate DNA access and must be lost before Msn2p can bind DNA. Together, these results highlight the complexities of stress-dependent chromatin changes and their effects on gene expression.
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83
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Chronic stress decreases availability of heat shock proteins to glucocorticoid receptor in response to novel acute stress in Wistar rat hypothalamus. Cell Mol Neurobiol 2012; 32:625-32. [PMID: 22350213 DOI: 10.1007/s10571-012-9811-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
Chronic psychosocial isolation (CPSI) is known to cause several maladaptive changes in the limbic brain structures, which regulate the hypothalamic-pituitary-adrenal (HPA) axis activity. In this study, we focused our investigation on CPSI effects in the hypothalamus (HT) since it is a major driver of HPA axis activity. We also investigated whether the exposure to CPSI could alter the response to subsequent acute stress (30-min immobilization). In the HT, we followed cytosolic and nuclear levels of the glucocorticoid receptor (GR), as a mediator of HPA axis feedback inhibition, and its chaperones, the heat shock proteins (HSPs), hsp70 and hsp90. The CPSI did not cause any changes in either GR or HSPs levels. However, we observed increase of the GR and hsp70 in both HT cellular compartments as a response of naïve rats to acute stress, whereas the response of CPSI rats to acute stress was associated with elevation of the GR in the cytosol and decrease of HSPs in the nucleus. Thus, our data indicated reduced availability of HSPs to GR in both cytosol and nucleus of the HT under acute stress of CPSI animals, and therefore, pointed out to potentially negative effects of CPSI on GR function in the HT.
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84
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Simons SS, Chow CC. The road less traveled: new views of steroid receptor action from the path of dose-response curves. Mol Cell Endocrinol 2012; 348:373-82. [PMID: 21664235 PMCID: PMC3184374 DOI: 10.1016/j.mce.2011.05.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/28/2011] [Accepted: 05/13/2011] [Indexed: 10/25/2022]
Abstract
Conventional studies of steroid hormone action proceed via quantitation of the maximal activity for gene induction at saturating concentrations of agonist steroid (i.e., A(max)). Less frequently analyzed parameters of receptor-mediated gene expression are EC(50) and PAA. The EC(50) is the concentration of steroid required for half-maximal agonist activity and is readily determined from the dose-response curve. The PAA is the partial agonist activity of an antagonist steroid, expressed as percent of A(max) under the same conditions. Recent results demonstrate that new and otherwise inaccessible mechanistic information is obtained when the EC(50) and/or PAA are examined in addition to the A(max). Specifically, A(max), EC(50), and PAA can be independently regulated, which suggests that novel pathways and factors may preferentially modify the EC(50) and/or PAA with little effect on A(max). Other approaches indicate that the activity of receptor-bound factors can be altered without changing the binding of factors to receptor. Finally, a new theoretical model of steroid hormone action not only permits a mechanistically based definition of factor activity but also allows the positioning of when a factor acts, as opposed to binds, relative to a kinetically defined step. These advances illustrate some of the benefits of expanding the mechanistic studies of steroid hormone action to routinely include EC(50) and PAA.
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Affiliation(s)
- S Stoney Simons
- Steroid Hormones Section, NIDDK/CEB, NIDDK, National Institutes of Health, Bethesda, MD 20892-1772, United States.
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85
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Conway-Campbell BL, Pooley JR, Hager GL, Lightman SL. Molecular dynamics of ultradian glucocorticoid receptor action. Mol Cell Endocrinol 2012; 348:383-93. [PMID: 21872640 DOI: 10.1016/j.mce.2011.08.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/19/2011] [Accepted: 08/12/2011] [Indexed: 01/08/2023]
Abstract
In recent years it has become evident that glucocorticoid receptor (GR) action in the nucleus is highly dynamic, characterized by a rapid exchange at the chromatin template. This stochastic mode of GR action couples perfectly with a deterministic pulsatile availability of endogenous ligand in vivo. The endogenous glucocorticoid hormone (cortisol in man and corticosterone in rodent) is secreted from the adrenal gland with an ultradian rhythm made up of pulses at approximately hourly intervals. These two components - the rapidly fluctuating ligand and the rapidly exchanging receptor - appear to have evolved to establish and maintain a system that is exquisitely responsive to the physiological demands of the organism. In this review, we discuss recent and innovative work that questions the idea of steady state, static hormone receptor responses, and replaces them with new concepts of stochastic mechanisms and oscillatory activity essential for optimal function in molecular and cellular systems.
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Affiliation(s)
- Becky L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, UK.
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86
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Mueller F, Karpova TS, Mazza D, McNally JG. Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching. Methods Mol Biol 2012; 833:153-76. [PMID: 22183594 DOI: 10.1007/978-1-61779-477-3_11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Fluorescence recovery after photobleaching (FRAP) has now become widely used to investigate nuclear protein binding to chromatin in live cells. FRAP can be applied qualitatively to assess if chromatin binding interactions are altered by various biological perturbations. It can also be applied semi-quantitatively to allow numerical comparisons between FRAP curves, and even fully quantitatively to yield estimates of in vivo diffusion constants and nuclear protein binding rates to chromatin. Here we describe how FRAP data should be collected and processed for these qualitative, semi-quantitative, and quantitative analyses.
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Affiliation(s)
- Florian Mueller
- Groupe Imagerie et Modélisation, Institut Pasteur, CNRS, URA 2582, Paris, France
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87
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Simpson NE, Gertz J, Imberg K, Myers RM, Garabedian MJ. Research resource: enhanced genome-wide occupancy of estrogen receptor α by the cochaperone p23 in breast cancer cells. Mol Endocrinol 2011; 26:194-202. [PMID: 22074947 DOI: 10.1210/me.2011-1068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
p23 is a chaperone with multiple heat shock protein 90 dependent and independent cellular functions, including stabilizing unliganded steroid receptors and modulating receptor-DNA dynamics. p23 protein is also up-regulated in several cancers, notably breast cancer. We previously demonstrated that higher expression of p23 in the estrogen-dependent breast cancer line MCF-7 (MCF-7+p23) selectively increased estrogen receptor (ER) target gene transcription and ER recruitment to regulatory elements, promoted cell invasion, and predicted a poor prognosis in breast cancer patients. To probe the impact of p23 on ER binding throughout the human genome, we compared ER occupancy in MCF-7+p23 cells relative to MCF-7-control cells by using chromatin immunoprecipitation followed by ultrahigh-throughput DNA sequencing in the absence and presence of 17β-estradiol (E2) treatment. We found that increased expression of p23 resulted in a 230% increase in the number of E2-induced ER-binding sites throughout the genome compared with control cells and also increased ER binding under basal conditions. Motif analysis indicated that ER binds to a similar DNA sequence regardless of p23 status. We also observed that ER tends to bind closer to genes that were induced, rather than repressed by either E2 treatment or p23 overexpression. Interestingly, we also found that the increased invasion of MCF-7+p23 cells was not only p23 dependent but also ER dependent. Thus, a small increase in the expression of p23 amplifies ER-binding genome wide and, in combination with ER, elicits an invasive phenotype. This makes p23 an attractive target for combating tumor cell metastasis in breast cancer patients.
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Affiliation(s)
- Natalie E Simpson
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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88
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Assembly of the transcription machinery: ordered and stable, random and dynamic, or both? Chromosoma 2011; 120:533-45. [PMID: 22048163 DOI: 10.1007/s00412-011-0340-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 01/12/2023]
Abstract
The assembly of the transcription machinery is a key step in gene activation, but even basic details of this process remain unclear. Here we discuss the apparent discrepancy between the classic sequential assembly model based mostly on biochemistry and an emerging dynamic assembly model based mostly on fluorescence microscopy. The former model favors a stable transcription complex with subunits that cooperatively assemble in order, whereas the latter model favors an unstable complex with subunits that may assemble more randomly. To confront this apparent discrepancy, we review the merits and drawbacks of the different experimental approaches and list potential biasing factors that could be responsible for the different interpretations of assembly. We then discuss how these biases might be overcome in the future with improved experiments or new techniques. Finally, we discuss how kinetic models for assembly may help resolve the ordered and stable vs. random and dynamic assembly debate.
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89
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Agricola E, Randall RA, Gaarenstroom T, Dupont S, Hill CS. Recruitment of TIF1γ to chromatin via its PHD finger-bromodomain activates its ubiquitin ligase and transcriptional repressor activities. Mol Cell 2011; 43:85-96. [PMID: 21726812 DOI: 10.1016/j.molcel.2011.05.020] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 03/05/2011] [Accepted: 05/02/2011] [Indexed: 02/05/2023]
Abstract
The interplay between sequence-specific DNA-binding transcription factors, histone-modifying enzymes, and chromatin-remodeling enzymes underpins transcriptional regulation. Although it is known how single domains of chromatin "readers" bind specific histone modifications, how combinations of histone marks are recognized and decoded is poorly understood. Moreover, the role of histone binding in regulating the enzymatic activity of chromatin readers is not known. Here we focus on the TGF-β superfamily transcriptional repressor TIF1γ/TRIM33/Ectodermin and demonstrate that its PHD finger-bromodomain constitutes a multivalent histone-binding module that specifically binds histone H3 tails unmethylated at K4 and R2 and acetylated at two key lysines. TIF1γ's ability to ubiquitinate its substrate Smad4 requires its PHD finger-bromodomain, as does its transcriptional repressor activity. Most importantly, TIF1γ's E3 ubiquitin ligase activity is induced by histone binding. We propose a model of TIF1γ activity in which it dictates the residence time of activated Smad complexes at promoters of TGF-β superfamily target genes.
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Affiliation(s)
- Eleonora Agricola
- Laboratory of Developmental Signalling, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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90
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Application of ChIP-Seq and related techniques to the study of immune function. Immunity 2011; 34:830-42. [PMID: 21703538 DOI: 10.1016/j.immuni.2011.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 01/02/2023]
Abstract
Behaviors observed at the cellular level such as development and acquisition of effector functions by immune cells result from transcriptional changes. The biochemical mediators of transcription are sequence-specific transcription factors (TFs), chromatin modifying enzymes, and chromatin, the complex of DNA and histone proteins. Covalent modification of DNA and histones, also termed epigenetic modification, influences the accessibility of target sequences for transcription factors on chromatin and the expression of linked genes required for immune functions. Genome-wide techniques such as ChIP-Seq have described the entire "cistrome" of transcription factors involved in specific developmental steps of B and T cells and started to define specific immune responses in terms of the binding profiles of critical effectors and epigenetic modification patterns. Current data suggest that both promoters and enhancers are prepared for action at different stages of activation by epigenetic modification through distinct transcription factors in different cells.
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91
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Ali F, Hindley C, McDowell G, Deibler R, Jones A, Kirschner M, Guillemot F, Philpott A. Cell cycle-regulated multi-site phosphorylation of Neurogenin 2 coordinates cell cycling with differentiation during neurogenesis. Development 2011; 138:4267-77. [PMID: 21852393 DOI: 10.1242/dev.067900] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During development of the central nervous system, the transition from progenitor maintenance to differentiation is directly triggered by a lengthening of the cell cycle that occurs as development progresses. However, the mechanistic basis of this regulation is unknown. The proneural transcription factor Neurogenin 2 (Ngn2) acts as a master regulator of neuronal differentiation. Here, we demonstrate that Ngn2 is phosphorylated on multiple serine-proline sites in response to rising cyclin-dependent kinase (cdk) levels. This multi-site phosphorylation results in quantitative inhibition of the ability of Ngn2 to induce neurogenesis in vivo and in vitro. Mechanistically, multi-site phosphorylation inhibits binding of Ngn2 to E box DNA, and inhibition of DNA binding depends on the number of phosphorylation sites available, quantitatively controlling promoter occupancy in a rheostat-like manner. Neuronal differentiation driven by a mutant of Ngn2 that cannot be phosphorylated by cdks is no longer inhibited by elevated cdk kinase levels. Additionally, phosphomutant Ngn2-driven neuronal differentiation shows a reduced requirement for the presence of cdk inhibitors. From these results, we propose a model whereby multi-site cdk-dependent phosphorylation of Ngn2 interprets cdk levels to control neuronal differentiation in response to cell cycle lengthening during development.
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Affiliation(s)
- Fahad Ali
- Department of Oncology, University of Cambridge, Hutchison/Medical Research Council Research Centre, Cambridge CB2 0XZ, UK
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92
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Matthews L, Johnson J, Berry A, Trebble P, Cookson A, Spiller D, Rivers C, Norman M, White M, Ray D. Cell cycle phase regulates glucocorticoid receptor function. PLoS One 2011; 6:e22289. [PMID: 21829454 PMCID: PMC3146484 DOI: 10.1371/journal.pone.0022289] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/23/2011] [Indexed: 11/18/2022] Open
Abstract
The glucocorticoid receptor (GR) is a member of the nuclear hormone receptor superfamily of ligand-activated transcription factors. In contrast to many other nuclear receptors, GR is thought to be exclusively cytoplasmic in quiescent cells, and only translocate to the nucleus on ligand binding. We now demonstrate significant nuclear GR in the absence of ligand, which requires nuclear localisation signal 1 (NLS1). Live cell imaging reveals dramatic GR import into the nucleus through interphase and rapid exclusion of the GR from the nucleus at the onset of mitosis, which persists into early G(1). This suggests that the heterogeneity in GR distribution is reflective of cell cycle phase. The impact of cell cycle-driven GR trafficking on a panel of glucocorticoid actions was profiled. In G2/M-enriched cells there was marked prolongation of glucocorticoid-induced ERK activation. This was accompanied by DNA template-specific, ligand-independent GR transactivation. Using chimeric and domain-deleted receptors we demonstrate that this transactivation effect is mediated by the AF1 transactivation domain. AF-1 harbours multiple phosphorylation sites, which are consensus sequences for kinases including CDKs, whose activity changes during the cell cycle. In G2/M there was clear ligand independent induction of GR phosphorylation on residues 203 and 211, both of which are phosphorylated after ligand activation. Ligand-independent transactivation required induction of phospho-S211GR but not S203GR, thereby directly linking cell cycle driven GR modification with altered GR function. Cell cycle phase therefore regulates GR localisation and post-translational modification which selectively impacts GR activity. This suggests that cell cycle phase is an important determinant in the cellular response to Gc, and that mitotic index contributes to tissue Gc sensitivity.
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Affiliation(s)
- Laura Matthews
- Developmental Biomedicine Research Group, University of Manchester, Manchester, United Kingdom
| | - James Johnson
- Centre for Cell Imaging, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Berry
- Developmental Biomedicine Research Group, University of Manchester, Manchester, United Kingdom
| | - Peter Trebble
- Developmental Biomedicine Research Group, University of Manchester, Manchester, United Kingdom
| | - Ann Cookson
- Developmental Biomedicine Research Group, University of Manchester, Manchester, United Kingdom
| | - Dave Spiller
- Centre for Cell Imaging, University of Liverpool, Liverpool, United Kingdom
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Caroline Rivers
- Division of Medicine, University of Bristol, Bristol, United Kingdom
| | - Michael Norman
- Division of Medicine, University of Bristol, Bristol, United Kingdom
| | - Mike White
- Centre for Cell Imaging, University of Liverpool, Liverpool, United Kingdom
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David Ray
- Developmental Biomedicine Research Group, University of Manchester, Manchester, United Kingdom
- * E-mail:
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93
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Abstract
Fluorescent protein labelling, as well as impressive progress in live cell imaging have revolutionised the view on how essential nuclear functions like gene transcription regulation and DNA repair are organised. Here, we address questions like how DNA-interacting molecules find and bind their target sequences in the vast amount of DNA. In addition, we discuss methods that have been developed for quantitative analysis of data from fluorescence recovery after photobleaching experiments (FRAP).
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94
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Conway-Campbell BL, George CL, Pooley JR, Knight DM, Norman MR, Hager GL, Lightman SL. The HSP90 molecular chaperone cycle regulates cyclical transcriptional dynamics of the glucocorticoid receptor and its coregulatory molecules CBP/p300 during ultradian ligand treatment. Mol Endocrinol 2011; 25:944-54. [PMID: 21511880 PMCID: PMC3163797 DOI: 10.1210/me.2010-0073] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
HSP90 regulates cyclical glucocorticoid receptor activity, cofactor recruitment, histone acetylation and transcriptional pulsing at the Period 1 promoter in response to ultradian glucocorticoid exposure. Glucocorticoid (GC) hormones are secreted from the adrenal gland in a characteristic pulsatile pattern. This ultradian secretory activity exhibits remarkable plasticity, with distinct changes in response to both physiological and stressful stimuli in humans and experimental animals. It is therefore important to understand how the pattern of GC exposure regulates intracellular signaling through the GC receptor (GR). We have previously shown that each pulse of ligand initiates rapid, transient GR activation in several physiologically relevant and functionally diverse target cell types. Using chromatin immunoprecipitation assays, we detect cyclical shifts in the net equilibrium position of GR association with regulatory elements of GC-target genes and have investigated in detail the mechanism of pulsatile transcriptional regulation of the GC-induced Period 1 gene. Transient recruitment of the histone acetyl transferase complex cAMP response element-binding protein (CREB) binding protein (CBP)/p300 is found to precisely track the ultradian hormone rhythm, resulting in transient localized net changes in lysine acetylation at GC-regulatory regions after each pulse. Pulsatile changes in histone H4 acetylation and concomitant recruitment of RNA polymerase 2 precede ultradian bursts of Period 1 gene transcription. Finally, we report the crucial underlying role of the intranuclear heat shock protein 90 molecular chaperone complex in pulsatile GR regulation. Pharmacological interference of heat shock protein 90 (HSP90) with geldanamycin during the intranuclear chaperone cycle completely ablated GR's cyclical activity, cyclical cAMP response element-binding protein (CREB) binding protein (CBP)/p300 recruitment, and the associated cyclical acetylation at the promoter region. These data imply a key role for an intact nuclear chaperone cycle in cyclical transcriptional responses, regulated in time by the pattern of pulsatile hormone.
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Affiliation(s)
- Becky L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, United Kingdom.
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95
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Intranuclear dynamics of corticosteroid receptors and effects of proteasomal activity in cultured hippocampal neural cells. Neurosci Lett 2011; 494:65-9. [DOI: 10.1016/j.neulet.2011.02.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/15/2011] [Accepted: 02/21/2011] [Indexed: 11/19/2022]
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96
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Nishi M. Dynamics of corticosteroid receptors: lessons from live cell imaging. Acta Histochem Cytochem 2011; 44:1-7. [PMID: 21448312 PMCID: PMC3061448 DOI: 10.1267/ahc.10028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 10/05/2010] [Indexed: 01/24/2023] Open
Abstract
Adrenal corticosteroids (cortisol in humans or corticosterone in rodents) exert numerous effects on the central nervous system that regulates the stress response, mood, learning and memory, and various neuroendocrine functions. Corticosterone (CORT) actions in the brain are mediated via two receptor systems: the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR). It has been shown that GR and MR are highly colocalized in the hippocampus. These receptors are mainly distributed in the cytoplasm without hormones and translocated into the nucleus after treatment with hormones to act as transcriptional factors. Thus the subcellular dynamics of both receptors are one of the most important issues. Given the differential action of MR and GR in the central nervous system, it is of great consequence to clarify how these receptors are trafficked between cytoplasm and nucleus and their interactions are regulated by hormones and/or other molecules to exert their transcriptional activity. In this review, we focus on the nucleocytoplasmic and subnuclear trafficking of GR and MR in neural cells and non-neural cells analyzed by using molecular imaging techniques with green fluorescent protein (GFP) including fluorescence recovery after photobleaching (FRAP) and fluorescence resonance energy transfer (FRET), and discuss various factors affecting the dynamics of these receptors. Furthermore, we discuss the future directions of in vivo molecular imaging of corticosteroid receptors at the whole brain level.
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Affiliation(s)
- Mayumi Nishi
- Department of Anatomy and Cell Biology, Nara Medical University
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97
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Scharf A, Grozdanov PN, Veith R, Kubitscheck U, Meier UT, von Mikecz A. Distant positioning of proteasomal proteolysis relative to actively transcribed genes. Nucleic Acids Res 2011; 39:4612-27. [PMID: 21306993 PMCID: PMC3113580 DOI: 10.1093/nar/gkr069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While it is widely acknowledged that the ubiquitin–proteasome system plays an important role in transcription, little is known concerning the mechanistic basis, in particular the spatial organization of proteasome-dependent proteolysis at the transcription site. Here, we show that proteasomal activity and tetraubiquitinated proteins concentrate to nucleoplasmic microenvironments in the euchromatin. Such proteolytic domains are immobile and distinctly positioned in relation to transcriptional processes. Analysis of gene arrays and early genes in Caenorhabditis elegans embryos reveals that proteasomes and proteasomal activity are distantly located relative to transcriptionally active genes. In contrast, transcriptional inhibition generally induces local overlap of proteolytic microdomains with components of the transcription machinery and degradation of RNA polymerase II. The results establish that spatial organization of proteasomal activity differs with respect to distinct phases of the transcription cycle in at least some genes, and thus might contribute to the plasticity of gene expression in response to environmental stimuli.
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Affiliation(s)
- Andrea Scharf
- IUF - Leibniz Research Institute for Environmental Medicine at Heinrich-Heine University Duesseldorf, D-40225 Duesseldorf, Germany
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98
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Oakley RH, Cidlowski JA. Cellular processing of the glucocorticoid receptor gene and protein: new mechanisms for generating tissue-specific actions of glucocorticoids. J Biol Chem 2011; 286:3177-84. [PMID: 21149445 PMCID: PMC3030321 DOI: 10.1074/jbc.r110.179325] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glucocorticoids regulate numerous physiological processes and are mainstays in the treatment of inflammation, autoimmune disease, and cancer. The traditional view that glucocorticoids act through a single glucocorticoid receptor (GR) protein has changed in recent years with the discovery of a large cohort of receptor subtypes arising from alternative processing of the GR gene. These isoforms differ in their expression, gene regulatory, and functional profiles. Post-translational modification of these proteins further expands GR diversity. Here, we discuss the origin and molecular properties of the GR isoforms and their contribution to the sensitivity and specificity of the glucocorticoid response.
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Affiliation(s)
- Robert H. Oakley
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Heath, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - John A. Cidlowski
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Heath, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
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99
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McMaster A, Jangani M, Sommer P, Han N, Brass A, Beesley S, Lu W, Berry A, Loudon A, Donn R, Ray DW. Ultradian cortisol pulsatility encodes a distinct, biologically important signal. PLoS One 2011; 6:e15766. [PMID: 21267416 PMCID: PMC3022879 DOI: 10.1371/journal.pone.0015766] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 11/28/2010] [Indexed: 11/19/2022] Open
Abstract
Context Cortisol is released in ultradian pulses. The biological relevance of the resulting fluctuating cortisol concentration has not been explored. Objective Determination of the biological consequences of ultradian cortisol pulsatility. Design A novel flow through cell culture system was developed to deliver ultradian pulsed or continuous cortisol to cells. The effects of cortisol dynamics on cell proliferation and survival, and on gene expression were determined. In addition, effects on glucocorticoid receptor (GR) expression levels and phosphorylation, as a potential mediator, were measured. Results Pulsatile cortisol caused a significant reduction in cell survival compared to continuous exposure of the same cumulative dose, due to increased apoptosis. Comprehensive analysis of the transcriptome response by microarray identified genes with a differential response to pulsatile versus continuous glucocorticoid delivery. These were confirmed with qRT-PCR. Several transcription factor binding sites were enriched in these differentially regulated target genes, including CCAAT-displacement protein (CDP). A CDP regulated reporter gene (MMTV-luc) was, as predicted, also differentially regulated by pulsatile compared to continuous cortisol delivery. Importantly there was no effect of cortisol delivery kinetics on either GR expression, or activation (GR phosphoSer211). Conclusions Cortisol oscillations exert important effects on target cell gene expression, and phenotype. This is not due to differences in cumulative cortisol exposure, or either expression, or activation of the GR. This suggests a novel means to regulate GR function.
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Affiliation(s)
- Andrew McMaster
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- The Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Maryam Jangani
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- The Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Paula Sommer
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Kwa-Zulu, Durban, South Africa
| | - Namshik Han
- Faculty of Life Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- School of Computer Science, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Andy Brass
- Faculty of Life Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- School of Computer Science, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Stephen Beesley
- Faculty of Life Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Weiqun Lu
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Faculty of Life Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Andrew Berry
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- The Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Andrew Loudon
- Faculty of Life Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Rachelle Donn
- The Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- * E-mail: (DWR); (RD)
| | - David W. Ray
- Endocrine Sciences Research Group, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- * E-mail: (DWR); (RD)
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100
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Abstract
The steady state dose-response curve of ligand-mediated gene induction usually appears to precisely follow a first-order Hill equation (Hill coefficient equal to 1). Additionally, various cofactors/reagents can affect both the potency and the maximum activity of gene induction in a gene-specific manner. Recently, we have developed a general theory for which an unspecified sequence of steps or reactions yields a first-order Hill dose-response curve (FHDC) for plots of the final product versus initial agonist concentration. The theory requires only that individual reactions "dissociate" from the downstream reactions leading to the final product, which implies that intermediate complexes are weakly bound or exist only transiently. We show how the theory can be utilized to make predictions of previously unidentified mechanisms and the site of action of cofactors/reagents. The theory is general and can be applied to any biochemical reaction that has a FHDC.
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Affiliation(s)
- Carson C Chow
- Laboratory of Biological Modeling, NIDDK/CEB, National Institutes of Health, Bethesda, Maryland, USA
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