1
|
Abstract
The world is continuously being transformed by science and technology (S&T), but to deliver equitable benefits to the public, scientists must be embedded in influential sectors of society-policy, diplomacy, journalism, law, business, education, and more. This means injecting PhD-level experts at every stage of research and development, from ideation, investigation, and investment to manufacture, deployment, regulation, and after-market evaluation.
Collapse
Affiliation(s)
- Keith R Yamamoto
- Keith R. Yamamoto is a professor in the Department of Cellular and Molecular Pharmacology at the University of California, San Francisco (UCSF), and vice chancellor for Science Policy and Strategy and director of Precision Medicine, UCSF, San Franciso, CA, USA. He is also the president of AAAS, Washington, DC, USA
| |
Collapse
|
2
|
Wailoo KA, Dzau VJ, Yamamoto KR. Embed equity throughout innovation. Science 2023; 381:1029. [PMID: 37676960 DOI: 10.1126/science.adk6365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The social benefit of technologies is frequently unevenly realized across the United States. Rural communities, individuals with disabilities, and historically marginalized groups face out-of-reach costs or lack access to products that meet their needs. Blame is typically placed on complicated regulatory processes or complex delivery systems, but this response neglects the problem that equity is not baked into the nation's innovation process at any stage. The United States needs to rethink its entire innovation ecosystem to incorporate equity as a foundational guiding principle-from research design and funding requirements to policies and regulations that govern the delivery and oversight of new products to the public.
Collapse
Affiliation(s)
- Keith A Wailoo
- Keith A. Wailoo is Henry Putnam University Professor of History and Public Affairs at Princeton University, Princeton, NJ, USA
| | - Victor J Dzau
- Victor J. Dzau is president of the National Academy of Medicine, Washington, DC, USA
| | - Keith R Yamamoto
- Keith R. Yamamoto is vice chancellor for Science Policy and Strategy and director of Precision Medicine at the University of California, San Francisco, CA, USA. He is president of the American Association for the Advancement of Science (the publisher of Science), Washington, DC, USA
| |
Collapse
|
3
|
Yamamoto KR. Institutions' role in trainee success. Science 2023; 379:1308. [PMID: 36996226 DOI: 10.1126/science.adh3723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Affiliation(s)
- Keith R Yamamoto
- Science Policy & Strategy, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
4
|
Ehmsen KT, Knuesel MT, Martinez D, Asahina M, Aridomi H, Yamamoto KR. Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements. Nucleic Acids Res 2021; 49:9117-9131. [PMID: 34417596 PMCID: PMC8450113 DOI: 10.1093/nar/gkab700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Unequivocal functional assessment of candidate genomic regulatory regions, such as transcriptional response elements, requires genetic alteration at their native chromosomal loci. Targeted DNA cleavage by Cas9 or other programmable nucleases enables analysis at virtually any genomic region, and diverse alleles generated by editing can be defined by deep sequencing for functional analysis. Interpretation of disrupted response elements, however, presents a special challenge, as these regions typically comprise clustered DNA binding motifs for multiple transcriptional regulatory factors (TFs); DNA sequence differences, natural or engineered, that affect binding by one TF can confer loss or gain of binding sites for other TFs. To address these and other analytical complexities, we created three computational tools that together integrate, in a single experiment, allele definition and TF binding motif evaluation for up to 9216 clones isolated, sequenced and propagated from Cas9-treated cell populations. We demonstrate 1) the capacity to functionally assess edited TF binding sites to query response element function, and 2) the efficacy and utility of these tools, by analyzing cell populations targeted by Cas9 for disruption of example glucocorticoid receptor (GR) binding motifs near FKBP5, a GR-regulated gene in the human adenocarcinoma cell line A549.
Collapse
Affiliation(s)
- Kirk T Ehmsen
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| | - Matthew T Knuesel
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| | - Delsy Martinez
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| | - Masako Asahina
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| | - Haruna Aridomi
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 600 16th Street, GH S572D, Box 2280, San Francisco, CA 94143-2280, USA
| |
Collapse
|
5
|
Sim I, Stebbins M, Bierer BE, Butte AJ, Drazen J, Dzau V, Hernandez AF, Krumholz HM, Lo B, Munos B, Perakslis E, Rockhold F, Ross JS, Terry SF, Yamamoto KR, Zarin DA, Li R. Time for NIH to lead on data sharing. Science 2020; 367:1308-1309. [DOI: 10.1126/science.aba4456] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ida Sim
- University of California San Francisco, San Francisco, CA, USA
- Vivli, Cambridge, MA, USA
| | | | - Barbara E. Bierer
- Multi-Regional Clinical Trials Center of Brigham and Women's Hospital and Harvard University, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Atul J. Butte
- University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Drazen
- Pulmonary and Communications Divisions, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Victor Dzau
- National Academy of Medicine, Washington, DC, USA
| | | | | | | | | | | | | | | | | | | | - Deborah A. Zarin
- Multi-Regional Clinical Trials Center of Brigham and Women's Hospital and Harvard University, Cambridge, MA, USA
| | - Rebecca Li
- Vivli, Cambridge, MA, USA
- Center for Bioethics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
6
|
Schnoes AM, Caliendo A, Morand J, Dillinger T, Naffziger-Hirsch M, Moses B, Gibeling JC, Yamamoto KR, Lindstaedt B, McGee R, O'Brien TC. Internship Experiences Contribute to Confident Career Decision Making for Doctoral Students in the Life Sciences. CBE Life Sci Educ 2018; 17:17/1/ar16. [PMID: 29449270 PMCID: PMC6007763 DOI: 10.1187/cbe.17-08-0164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/26/2017] [Accepted: 01/05/2018] [Indexed: 05/25/2023]
Abstract
The Graduate Student Internships for Career Exploration (GSICE) program at the University of California, San Francisco (UCSF), offers structured training and hands-on experience through internships for a broad range of PhD-level careers. The GSICE program model was successfully replicated at the University of California, Davis (UC Davis). Here, we present outcome data for a total of 217 PhD students participating in the UCSF and UC Davis programs from 2010 to 2015 and 2014 to 2015, respectively. The internship programs at the two sites demonstrated comparable participation, internship completion rates, and overall outcomes. Using survey, focus group, and individual interview data, we find that the programs provide students with career development skills, while increasing students' confidence in career exploration and decision making. Internships, in particular, were perceived by students to increase their ability to discern a career area of choice and to increase confidence in pursuing that career. We present data showing that program participation does not change median time to degree and may help some trainees avoid "default postdocs." Our findings suggest important strategies for institutions developing internship programs for PhD students, namely: including a structured training component, allowing postgraduation internships, and providing a central organization point for internship programs.
Collapse
Affiliation(s)
- Alexandra M Schnoes
- University of California, San Francisco, San Francisco, CA 94143
- iBiology, San Francisco, CA 94143
| | - Anne Caliendo
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | | | | | | | - Bruce Moses
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | | | - Keith R Yamamoto
- University of California, San Francisco, San Francisco, CA 94143
| | - Bill Lindstaedt
- University of California, San Francisco, San Francisco, CA 94143
| | - Richard McGee
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | | |
Collapse
|
7
|
Abstract
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity. This structural and mechanistic perspective on GR regulatory specificity is likely to extend to other eukaryotic TRFs.
Collapse
Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Matthew T Knuesel
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
| |
Collapse
|
8
|
Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH. Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Res 2017; 45:1805-1819. [PMID: 27903902 PMCID: PMC5389550 DOI: 10.1093/nar/gkw1163] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study the role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within the universe of accessible chromatin. Taken together, our results uncovered that although GR preferentially binds accessible chromatin, its binding is biased against accessible chromatin located at promoter regions. This bias can only be explained partially by the presence of fewer GR recognition sequences, arguing for the existence of additional mechanisms that interfere with GR binding at promoters. Therefore, we tested the role of H3K9ac, the chromatin feature with the strongest negative association with GR binding, but found that this correlation does not reflect a causative link. Finally, we find a higher percentage of promoter-proximal GR binding for genes regulated by GR across cell types than for cell type-specific target genes. Given that GR almost exclusively binds accessible chromatin, we propose that cell type-specific regulation by GR preferentially occurs via distal enhancers, whose chromatin accessibility is typically cell type-specific, whereas ubiquitous target gene regulation is more likely to result from binding to promoter regions, which are often accessible regardless of cell type examined.
Collapse
Affiliation(s)
- Michael I. Love
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
- Department of Biostatistics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Matthew R. Huska
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Marcel Jurk
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Stephan R. Starick
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Kevin Schwahn
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Samantha B. Cooper
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Morgane Thomas-Chollier
- Computational Systems Biology, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | | |
Collapse
|
9
|
Walter P, Yamamoto KR. Science as a Way of Knowing: From Protein Machines to Evidence-Based Decisions. Cell 2016; 167:16-19. [PMID: 27634318 DOI: 10.1016/j.cell.2016.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 2016 Lasker∼Koshland Special Achievement Award will be presented to Bruce Alberts for a lifetime career of outstanding scientific discovery and inspiring leadership and mentorship in promoting fundamental research, science education, and rational, evidence-based values worldwide.
Collapse
Affiliation(s)
- Peter Walter
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA.
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
10
|
Dzau VJ, Ginsburg GS, Chopra A, Goldman D, Green ED, Leonard DGB, McClellan M, Plump A, Terry SF, Yamamoto KR. Realizing the Full Potential of Precision Medicine in Health and Health Care: A Vital Direction for Health and Health Care. NAM Perspect 2016. [DOI: 10.31478/201609k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Ratnappan R, Ward JD, Yamamoto KR, Ghazi A. Nuclear hormone receptors as mediators of metabolic adaptability following reproductive perturbations. Worm 2016; 5:e1151609. [PMID: 27073739 DOI: 10.1080/21624054.2016.1151609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/21/2016] [Accepted: 02/01/2016] [Indexed: 01/13/2023]
Abstract
Previously, we identified a group of nuclear hormone receptors (NHRs) that promote longevity in the nematode Caenorhabditis elegans following germline-stem cell (GSC) loss. This group included NHR-49, the worm protein that performs functions similar to vertebrate PPARα, a key regulator of lipid metabolism. We showed that NHR-49/PPARα enhances mitochondrial β-oxidation and fatty acid desaturation upon germline removal, and through the coordinated enhancement of these processes allows the animal to retain lipid homeostasis and undergo lifespan extension. NHR-49/PPARα expression is elevated in GSC-ablated animals, in part, by DAF-16/FOXO3A and TCER-1/TCERG1, two other conserved, pro-longevity transcriptional regulators that are essential for germline-less longevity. In exploring the roles of the other pro-longevity NHRs, we discovered that one of them, NHR-71/HNF4, physically interacted with NHR-49/PPARα. NHR-71/HNF4 did not have a broad impact on the expression of β-oxidation and desaturation targets of NHR-49/PPARα. But, both NHR-49/PPARα and NHR-71/HNF4 were essential for the increased expression of DAF-16/FOXO3A- and TCER-1/TCERG1-downstream target genes. In addition, nhr-49 inactivation caused a striking membrane localization of KRI-1, the only known common upstream regulator of DAF-16/FOXO3A and TCER-1/TCERG1, suggesting that it may operate in a positive feedback loop to potentiate the activity of this pathway. These data underscore how selective interactions between NHRs that function as nodes in metabolic networks, confer functional specificity in response to different physiological stimuli.
Collapse
Affiliation(s)
- Ramesh Ratnappan
- Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, PA, USA
| | - Jordan D Ward
- Department of Cellular and Molecular Pharmacology, University of California , San Francisco, San Francisco, CA, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California , San Francisco, San Francisco, CA, USA
| | - Arjumand Ghazi
- Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, PA, USA
| |
Collapse
|
12
|
Pack LR, Yamamoto KR, Fujimori DG. Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C). J Biol Chem 2016; 291:6060-70. [PMID: 26747609 DOI: 10.1074/jbc.m115.696864] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 12/23/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 9 trimethylation (H3K9me3) are epigenetic marks with opposing roles in transcription regulation. Whereas colocalization of these modifications is generally excluded in the genome, how this preclusion is established remains poorly understood. Lysine demethylase 4C (KDM4C), an H3K9me3 demethylase, localizes predominantly to H3K4me3-containing promoters through its hybrid tandem tudor domain (TTD) (1, 2), providing a model for how these modifications might be excluded. We quantitatively investigated the contribution of the TTD to the catalysis of H3K9me3 demethylation by KDM4C and demonstrated that TTD-mediated recognition of H3K4me3 stimulates demethylation of H3K9me3 in cis on peptide and mononucleosome substrates. Our findings support a multivalent interaction mechanism, by which an activating mark, H3K4me3, recruits and stimulates KDM4C to remove the repressive H3K9me3 mark, thus facilitating exclusion. In addition, our work suggests that differential TTD binding properties across the KDM4 demethylase family may differentiate their targets in the genome.
Collapse
Affiliation(s)
- Lindsey R Pack
- From the Department of Cellular and Molecular Pharmacology, the Tetrad Graduate Program, and
| | | | - Danica Galonić Fujimori
- From the Department of Cellular and Molecular Pharmacology, the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| |
Collapse
|
13
|
|
14
|
Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 2015; 348:36-8. [PMID: 25791083 DOI: 10.1126/science.aab1028] [Citation(s) in RCA: 305] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- David Baltimore
- California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125, USA
| | - Paul Berg
- Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA
| | - Michael Botchan
- University of California, Berkeley, 450 Li Ka Shing no. 3370, Berkeley, CA 94720-3370, USA. Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, USA
| | - R Alta Charo
- Department of Medical History and Bioethics, School of Medicine and Public Health, University of Wisconsin Law School, 975 Bascom Mall, Madison, WI 53706, USA
| | - George Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - George Q Daley
- Boston Children's Hospital, 300 Longwood Avenue, Karp Family Building, 7th Floor, Boston, MA 02115, USA. Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Jennifer A Doudna
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, 731 Stanley Hall, MS 3220, University of California, Berkeley, Berkeley, CA 94720-3220, USA.
| | - Marsha Fenner
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Henry T Greely
- Center for Law and the Biosciences, Crown Quadrangle 559 Nathan Abbott Way Stanford, CA 94305-8610, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - G Steven Martin
- Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, 210K Durant Hall, Berkeley, CA 94720-2920, USA
| | - Edward Penhoet
- Alta Partners, One Embarcadero Center, 37th Floor, San Francisco, CA 94111, USA
| | - Jennifer Puck
- Department of Pediatrics UCSF School of Medicine, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samuel H Sternberg
- Department of Chemistry, 731 Stanley Hall, MS 3220, University of California, Berkeley, CA 94720-3220, USA
| | - Jonathan S Weissman
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Keith R Yamamoto
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. UCSF School of Medicine, 600 16th Street, San Francisco, CA 94158, USA
| |
Collapse
|
15
|
Schiller BJ, Chodankar R, Watson LC, Stallcup MR, Yamamoto KR. Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. Genome Biol 2014; 15:418. [PMID: 25085117 PMCID: PMC4149261 DOI: 10.1186/s13059-014-0418-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/17/2014] [Indexed: 11/10/2022] Open
Abstract
Background Glucocorticoid receptor (GR) is a hormone-activated, DNA-binding transcriptional regulatory factor that controls inflammation, metabolism, stress responses, and other physiological processes. In vitro, GR binds as an inverted dimer to a motif consisting of two imperfectly palindromic 6 bp half sites separated by 3 bp spacers. In vivo, GR employs different patterns of functional surfaces of GR to regulate different target genes. The relationships between GR genomic binding and functional surface utilization have not been defined. Results We find that A477T, a GR mutant that disrupts the dimerization interface, differs from wild-type GRα in binding and regulation of target genes. Genomic regions strongly occupied by A477T are enriched for a novel half site motif. In vitro, GRα binds half sites as a monomer. Through the overlap between GRα- and A477T-bound regions, we identify GRα-bound regions containing only half sites. We further identify GR target genes linked with half sites and not with the full motif. Conclusions Genomic regions bound by GR differ in underlying DNA sequence motifs and in the GR functional surfaces employed for regulation. Identification of GR binding regions that selectively utilize particular GR surfaces may discriminate sub-motifs, including the half site motif, that favor those surfaces. This approach may contribute to predictive models for GR activity and therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0418-y) contains supplementary material, which is available to authorized users.
Collapse
|
16
|
Ward JD, Yamamoto KR, Asahina M. SUMO as a nuclear hormone receptor effector: New insights into combinatorial transcriptional regulation. Worm 2014; 3:e29317. [PMID: 25254154 DOI: 10.4161/worm.29317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022]
Abstract
Animal development is driven by robust, cell-specific gene expression programs. Understanding mechanistically how a single transcription factor (TF) can govern distinct programs with exquisite precision is a major challenge. We view TFs as signal integrators, taking information from co-regulator interactions, post-translational modifications, other transcription factors, chromatin state, DNA sequence and in some cases, specific noncovalent ligands, to determine the collection of genes regulated by a TF at any given time. Here, we describe a reductionist approach to combinatorial transcriptional regulation, focusing on a single C. elegans TF, the nuclear hormone receptor NHR-25, and a single post-translational modification, SUMO. We suggest that the ratio of sumoylated to unsumoylated NHR-25 could specify a switch-like cell-fate decision during vulval development. Direct examination of this "SUMO ratio" in vivo is challenging and we discuss possible solutions going forward. We also consider how sumoylation of multiple substrates might be coordinated during vulval development. Finally, we note that iteration of this approach could leverage our sumoylation findings to define the roles of other effectors of NHR-25 in the developing vulva and in other tissues.
Collapse
Affiliation(s)
- Jordan D Ward
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA
| | - Masako Asahina
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA ; Institute of Parasitology; Biology Centre ASCR; Ceske Budejovice, Czech Republic ; University of South Bohemia; Ceske Budejovice, Czech Republic
| |
Collapse
|
17
|
Ward JD, Bojanala N, Bernal T, Ashrafi K, Asahina M, Yamamoto KR. Sumoylated NHR-25/NR5A regulates cell fate during C. elegans vulval development. PLoS Genet 2013; 9:e1003992. [PMID: 24348269 PMCID: PMC3861103 DOI: 10.1371/journal.pgen.1003992] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022] Open
Abstract
Individual metazoan transcription factors (TFs) regulate distinct sets of genes depending on cell type and developmental or physiological context. The precise mechanisms by which regulatory information from ligands, genomic sequence elements, co-factors, and post-translational modifications are integrated by TFs remain challenging questions. Here, we examine how a single regulatory input, sumoylation, differentially modulates the activity of a conserved C. elegans nuclear hormone receptor, NHR-25, in different cell types. Through a combination of yeast two-hybrid analysis and in vitro biochemistry we identified the single C. elegans SUMO (SMO-1) as an NHR-25 interacting protein, and showed that NHR-25 is sumoylated on at least four lysines. Some of the sumoylation acceptor sites are in common with those of the NHR-25 mammalian orthologs SF-1 and LRH-1, demonstrating that sumoylation has been strongly conserved within the NR5A family. We showed that NHR-25 bound canonical SF-1 binding sequences to regulate transcription, and that NHR-25 activity was enhanced in vivo upon loss of sumoylation. Knockdown of smo-1 mimicked NHR-25 overexpression with respect to maintenance of the 3° cell fate in vulval precursor cells (VPCs) during development. Importantly, however, overexpression of unsumoylatable alleles of NHR-25 revealed that NHR-25 sumoylation is critical for maintaining 3° cell fate. Moreover, SUMO also conferred formation of a developmental time-dependent NHR-25 concentration gradient across the VPCs. That is, accumulation of GFP-tagged NHR-25 was uniform across VPCs at the beginning of development, but as cells began dividing, a smo-1-dependent NHR-25 gradient formed with highest levels in 1° fated VPCs, intermediate levels in 2° fated VPCs, and low levels in 3° fated VPCs. We conclude that sumoylation operates at multiple levels to affect NHR-25 activity in a highly coordinated spatial and temporal manner.
Collapse
Affiliation(s)
- Jordan D. Ward
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Nagagireesh Bojanala
- Institute of Parasitology, Biology Centre ASCR, Ceske Budejovice, Czech Republic
- University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Teresita Bernal
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Kaveh Ashrafi
- Department of Physiology, University of California San Francisco, San Francisco, California, United States of America
| | - Masako Asahina
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Institute of Parasitology, Biology Centre ASCR, Ceske Budejovice, Czech Republic
- University of South Bohemia, Ceske Budejovice, Czech Republic
- * E-mail: (MA); (KRY)
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MA); (KRY)
| |
Collapse
|
18
|
Ziv L, Muto A, Schoonheim PJ, Meijsing SH, Strasser D, Ingraham HA, Schaaf MJ, Yamamoto KR, Baier H. An affective disorder in zebrafish with mutation of the glucocorticoid receptor. Mol Psychiatry 2013; 18:681-91. [PMID: 22641177 PMCID: PMC4065652 DOI: 10.1038/mp.2012.64] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 03/26/2012] [Accepted: 04/03/2012] [Indexed: 11/25/2022]
Abstract
Upon binding of cortisol, the glucocorticoid receptor (GR) regulates the transcription of specific target genes, including those that encode the stress hormones corticotropin-releasing hormone (CRH) and adrenocorticotropic hormone. Dysregulation of the stress axis is a hallmark of major depression in human patients. However, it is still unclear how glucocorticoid signaling is linked to affective disorders. We identified an adult-viable zebrafish mutant in which the negative feedback on the stress response is disrupted, due to abolition of all transcriptional activity of GR. As a consequence, cortisol is elevated, but unable to signal through GR. When placed into an unfamiliar aquarium ('novel tank'), mutant fish become immobile ('freeze'), show reduced exploratory behavior and do not habituate to this stressor upon repeated exposure. Addition of the antidepressant fluoxetine to the holding water and social interactions restore normal behavior, followed by a delayed correction of cortisol levels. Fluoxetine does not affect the overall transcription of CRH, the mineralocorticoid receptor (MR), the serotonin transporter (Serta) or GR itself. Fluoxetine, however, suppresses the stress-induced upregulation of MR and Serta in both wild-type fish and mutants. Our studies show a conserved, protective function of glucocorticoid signaling in the regulation of emotional behavior and reveal novel molecular aspects of how chronic stress impacts vertebrate brain physiology and behavior. Importantly, the zebrafish model opens up the possibility of high-throughput drug screens in search of new classes of antidepressants.
Collapse
Affiliation(s)
- Limor Ziv
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Cancer Research Center, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Akira Muto
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
| | - Peter J. Schoonheim
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Sebastiaan H. Meijsing
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Daniel Strasser
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Holly A. Ingraham
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | | | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Herwig Baier
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Max Planck Institute of Neurobiology, Department Genes – Circuits – Behavior, Martinsried, Germany
| |
Collapse
|
19
|
Hood LE, Omenn GS, Moritz RL, Aebersold R, Yamamoto KR, Amos M, Hunter-Cevera J, Locascio L. New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics 2013; 12:2773-83. [PMID: 22807061 DOI: 10.1002/pmic.201270086] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14-15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.
Collapse
|
20
|
|
21
|
Holdorf MM, Cooper SB, Yamamoto KR, Miranda JJL. Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology 2011; 415:1-5. [PMID: 21550623 PMCID: PMC3808970 DOI: 10.1016/j.virol.2011.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 02/11/2011] [Accepted: 04/15/2011] [Indexed: 01/02/2023]
Abstract
The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences throughout the genome that are found not just proximal to the regulatory elements of latent genes, but also near lytic genes. In addition to tracking with known transcripts, RNA Polymerase II appears at two unannotated positions, one of which lies within the latent origin of replication. The widespread occupancy profile of each protein reveals binding near or at a myriad of regulatory elements and suggests context-dependent functions.
Collapse
MESH Headings
- Base Sequence
- CCCTC-Binding Factor
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/metabolism
- Epstein-Barr Virus Nuclear Antigens/genetics
- Epstein-Barr Virus Nuclear Antigens/metabolism
- Gene Expression Regulation, Viral
- Genome, Viral
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Herpesvirus 4, Human/physiology
- Humans
- Plasmids/genetics
- Promoter Regions, Genetic
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- Replication Origin/genetics
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Sequence Analysis, DNA
- Virus Latency
- Cohesins
Collapse
Affiliation(s)
- Meghan M. Holdorf
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - Samantha B. Cooper
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA 94158
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - JJL Miranda
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| |
Collapse
|
22
|
Ou CY, LaBonte MJ, Manegold PC, So AYL, Ianculescu I, Gerke DS, Yamamoto KR, Ladner RD, Kahn M, Kim JH, Stallcup MR. A coactivator role of CARM1 in the dysregulation of β-catenin activity in colorectal cancer cell growth and gene expression. Mol Cancer Res 2011; 9:660-70. [PMID: 21478268 DOI: 10.1158/1541-7786.mcr-10-0223] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Aberrant activation of Wnt/β-catenin signaling, resulting in the expression of Wnt-regulated oncogenes, is recognized as a critical factor in the etiology of colorectal cancer. Occupancy of β-catenin at promoters of Wnt target genes drives transcription, but the mechanism of β-catenin action remains poorly understood. Here, we show that CARM1 (coactivator-associated arginine methyltransferase 1) interacts with β-catenin and positively modulates β-catenin-mediated gene expression. In colorectal cancer cells with constitutively high Wnt/β-catenin activity, depletion of CARM1 inhibits expression of endogenous Wnt/β-catenin target genes and suppresses clonal survival and anchorage-independent growth. We also identified a colorectal cancer cell line (RKO) with a low basal level of β-catenin, which is dramatically elevated by treatment with Wnt3a. Wnt3a also increased the expression of a subset of endogenous Wnt target genes, and CARM1 was required for the Wnt-induced expression of these target genes and the accompanying dimethylation of arginine 17 of histone H3. Depletion of β-catenin from RKO cells diminished the Wnt-induced occupancy of CARM1 on a Wnt target gene, indicating that CARM1 is recruited to Wnt target genes through its interaction with β-catenin and contributes to transcriptional activation by mediating events (including histone H3 methylation) that are downstream from the actions of β-catenin. Therefore, CARM1 is an important positive modulator of Wnt/β-catenin transcription and neoplastic transformation, and may thereby represent a novel target for therapeutic intervention in cancers involving aberrantly activated Wnt/β-catenin signaling.
Collapse
Affiliation(s)
- Chen-Yin Ou
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Nuclear hormone receptors (NHRs) are proteins that regulate gene expression in response to developmental, environmental, and nutritional signals. The activity of some NHRs is selectively and reversibly modulated by small molecular weight compounds. However, for others - termed "orphan" receptors - no such ligands have (yet) been identified, and at least some NHRs may lack natural ligands. NHRs exhibit a stereotyped architecture, with conserved N-terminal DNA-binding domains (DBDs) and more variable C-terminal ligand-binding domains (LBDs). NHRs control the transcription of remarkably diverse and specific gene networks, apparently by integrating multiple regulatory inputs that interact with distinct receptor surfaces; these inputs include small molecule ligands, transcriptional coregulators, and response elements, the genomic sites to which the receptors bind. NHRs comprise an ancient superfamily found in all metazoans, and recent findings have revealed NHR-like regulatory factors in fungi. Here, we consider NHR function and evolution in nematodes, roundworms that inhabit terrestrial, marine, and freshwater habitats; we focus in particular on the well-established experimental organism Caenorhabditis elegans. Interestingly, the C. elegans genome encodes a massively expanded NHR family; we speculate that some of the multiple physiological activities governed by individual mammalian NHRs may be distributed among multiple members of the C. elegans family, potentially focusing and simplifying functional analyses. Accordingly, investigations of relevant NHR cofactors, ligands, and response elements might also prove to be simpler; moreover, the abbreviated intergenic regions of the C. elegans genome will facilitate the assignment of response elements to target genes. Finally, the growing interest in medically relevant nematodes is providing novel insights into the function and evolution of NHRs.
Collapse
Affiliation(s)
- Stefan Taubert
- Department of Medical Genetics, University of British Columbia; Centre for Molecular Medicine and Therapeutics; and Child & Family Research Institute, Vancouver, BC, Canada
| | - Jordan D. Ward
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Corresponding author: UCSF, 600 16 St, GH-S574, San Francisco CA 94143-2280; Phone: +1 (415) 476-8445;
| |
Collapse
|
24
|
Cvoro A, Yuan C, Paruthiyil S, Miller OH, Yamamoto KR, Leitman DC. Cross talk between glucocorticoid and estrogen receptors occurs at a subset of proinflammatory genes. J Immunol 2011; 186:4354-60. [PMID: 21357268 DOI: 10.4049/jimmunol.1002205] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glucocorticoids exert potent anti-inflammatory effects by repressing proinflammatory genes. We previously demonstrated that estrogens repress numerous proinflammatory genes in U2OS cells. The objective of this study was to determine if cross talk occurs between the glucocorticoid receptor (GR) and estrogen receptor (ER)α. The effects of dexamethasone (Dex) and estradiol on 23 proinflammatory genes were examined in human U2OS cells stably transfected with ERα or GR. Three classes of genes were regulated by ERα and/or GR. Thirteen genes were repressed by both estradiol and Dex (ER/GR-repressed genes). Five genes were repressed by ER (ER-only repressed genes), and another five genes were repressed by GR (GR-only repressed genes). To examine if cross talk occurs between ER and GR at ER/GR-repressed genes, U2OS-GR cells were infected with an adenovirus that expresses ERα. The ER antagonist, ICI 182780 (ICI), blocked Dex repression of ER/GR-repressed genes. ICI did not have any effect on the GR-only repressed genes or genes activated by Dex. These results demonstrate that ICI acts on subset of proinflammatory genes in the presence of ERα but not on GR-activated genes. ICI recruited ERα to the IL-8 promoter but did not prevent Dex recruitment of GR. ICI antagonized Dex repression of the TNF response element by blocking the recruitment of nuclear coactivator 2. These findings indicate that the ICI-ERα complex blocks Dex-mediated repression by interfering with nuclear coactivator 2 recruitment to GR. Our results suggest that it might be possible to exploit ER and GR cross talk for glucocorticoid therapies using drugs that interact with ERs.
Collapse
Affiliation(s)
- Aleksandra Cvoro
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | |
Collapse
|
25
|
Costa MJ, So AYL, Kaasik K, Krueger KC, Pillsbury ML, Fu YH, Ptacek LJ, Yamamoto KR, Feldman BJ. Circadian rhythm gene period 3 is an inhibitor of the adipocyte cell fate. J Biol Chem 2011; 286:9063-70. [PMID: 21228270 DOI: 10.1074/jbc.m110.164558] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Glucocorticoids rapidly and robustly induce cell fate decisions in various multipotent cells, although the precise mechanisms of these important cellular events are not understood. Here we showed that glucocorticoids repressed Per3 expression and that this repression was critical for advancing mesenchymal stem cells to the adipocyte fate. Exogenous expression of Per3 inhibited adipogenesis, whereas knocking out Per3 enhanced that fate. Moreover, we found that PER3 formed a complex with PPARγ and inhibited PPARγ-mediated transcriptional activation via Pparγ response elements. Consistent with these findings, Per3 knock-out mice displayed alterations in body composition, with both increased adipose and decreased muscle tissue compared with wild-type mice. Our findings identify Per3 as potent mediator of cell fate that functions by altering the transcriptional activity of PPARγ.
Collapse
Affiliation(s)
- Maria Jose Costa
- Department of Pediatrics, University, Stanford, California 94305, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJM. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol 2010; 6:367. [PMID: 20461074 PMCID: PMC2890327 DOI: 10.1038/msb.2010.23] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/26/2010] [Indexed: 12/15/2022] Open
Abstract
We present the first gene regulatory network (GRN) that pertains to post-developmental gene expression. Specifically, we mapped a transcription regulatory network of Caenorhabditis elegans metabolic gene promoters using gene-centered yeast one-hybrid assays. We found that the metabolic GRN is enriched for nuclear hormone receptors (NHRs) compared with other gene-centered regulatory networks, and that these NHRs organize into functional network modules. The NHR family has greatly expanded in nematodes; C. elegans has 284 NHRs, whereas humans have only 48. We show that the NHRs in the metabolic GRN have metabolic phenotypes, suggesting that they do not simply function redundantly. The mediator subunit MDT-15 preferentially interacts with NHRs that occur in the metabolic GRN. We describe an NHR circuit that responds to nutrient availability and propose a model for the evolution and organization of NHRs in C. elegans metabolic regulatory networks.
Physical and/or regulatory interactions between transcription factors (TFs) and their target genes are essential to establish body plans of multicellular organisms during development, and these interactions have been studied extensively in the context of GRNs. The precise control of differential gene expression is also of critical importance to maintain physiological homeostasis, and many metabolic disorders such as obesity and diabetes coincide with substantial changes in gene expression. Much work has focused on the GRNs that control metazoan development; however, the design principles and organization of the GRNs that control systems physiology remain largely unexplored. In this study, we present the first gene-centered GRN that includes ∼70 genes involved in C. elegans metabolism and physiology, 100 TFs and more than 500 protein–DNA interactions between them. The resulting metabolic GRN is enriched for NHRs, compared with other gene-centered regulatory networks. NHRs are well-known regulators of lipid meta-qj;bolism in mammals. The transcriptional activity of NHRs can be modified by diffusible ligands, which allows these TFs to function as molecular sensors and rapidly alter the expression of their target genes. Interestingly, NHRs comprise the largest family of TFs in nematodes; the C. elegans genome encodes 284 NHRs, most of which are uncharacterized. Furthermore, their organization in GRNs has not yet been investigated. In our study, we show that the C. elegans NHRs that we retrieved in the metabolic GRN organize into network modules, and that most of these NHRs function to maintain lipid homeostasis in the nematode. Interestingly, network modularity has been proposed to facilitate rapid and robust changes in gene expression. Our results suggest that the C. elegans metabolic GRN may have evolved by combining NHR family expansion with the specific modular wiring of NHRs to enable the rapid adaptation of the animal to different environmental cues. NHRs can interact with transcriptional cofactors such as chromatin remodeling complexes and Mediator components. For instance, the C. elegans Mediator subunit, MDT-15, can interact with NHR-49 to regulate the expression of its target genes. To find all the TFs that MDT-15 can interact with, we performed systematic yeast two-hybrid assays with MDT-15 versus 755 full-length TFs. We found that MDT-15 preferentially associates with NHRs, and specifically with those NHRs that confer a metabolic phenotype and that occur in the metabolic GRN. This illustrates the central role of MDT-15 in the regulation of metabolic gene expression. Using a variety of genetic and biochemical approaches, we characterized NHR-86 in more detail. NHR-86 participates in one of the two NHR modules, and has a high-flux capacity; that is it has both a high incoming and a high outgoing degree. We obtained an nhr-86 mutant and generated an NHR-86 antibody, and showed that NHR-86 functions as an auto-repressor in vivo and that nhr-86 mutant animals store abnormally high levels of body fat. Finally, we discovered a novel NHR circuit that responds to nutrient availability. In this circuit NHR-45 regulates the activity of nhr-178 promoter in two distinct physiologically important tissues: the intestine and the hypodermis. Both of these NHRs are required to maintain lipid homeostasis in C. elegans. The expression of nhr-178 is responsive to the nutritional status of the animal, which switches between ON and OFF states in the hypodermis. We found that NHR-45 activity is necessary to control this switch in the hypodermis. Interestingly, NHR-45 has opposite effects on the activity of the nhr-178 promoter in these tissues: NHR-45 activates this promoter in the intestine, but represses it in the hypodermis. Altogether our study leads to a model in which the expansion of the NHR family, TFs that have the capacity to act as fast molecular sensors, is combined with a modular network organization to enable rapid and robust responses to various environmental cues. Gene regulatory networks (GRNs) provide insights into the mechanisms of differential gene expression at a systems level. GRNs that relate to metazoan development have been studied extensively. However, little is still known about the design principles, organization and functionality of GRNs that control physiological processes such as metabolism, homeostasis and responses to environmental cues. In this study, we report the first experimentally mapped metazoan GRN of Caenorhabditis elegans metabolic genes. This network is enriched for nuclear hormone receptors (NHRs). The NHR family has greatly expanded in nematodes: humans have 48 NHRs, but C. elegans has 284, most of which are uncharacterized. We find that the C. elegans metabolic GRN is highly modular and that two GRN modules predominantly consist of NHRs. Network modularity has been proposed to facilitate a rapid response to different cues. As NHRs are metabolic sensors that are poised to respond to ligands, this suggests that C. elegans GRNs evolved to enable rapid and adaptive responses to different cues by a concurrence of NHR family expansion and modular GRN wiring.
Collapse
Affiliation(s)
- H Efsun Arda
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, Meijsing SH, Sancak Y, Cui X, Steine EJ, Miller JC, Tam P, Bartsevich VV, Meng X, Rupniewski I, Gopalan SM, Sun HC, Pitz KJ, Rock JM, Zhang L, Davis GD, Rebar EJ, Cheeseman IM, Yamamoto KR, Sabatini DM, Jaenisch R, Gregory PD, Urnov FD. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res 2010; 20:1133-42. [PMID: 20508142 DOI: 10.1101/gr.106773.110] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Isogenic settings are routine in model organisms, yet remain elusive for genetic experiments on human cells. We describe the use of designed zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into the PPP1R12C gene, a "safe harbor" locus known as AAVS1. ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including fibroblasts and hES cells. When added to this locus, transgenes such as expression cassettes for shRNAs, small-molecule-responsive cDNA expression cassettes, and reporter constructs, exhibit consistent expression and sustained function over 50 cell generations. By avoiding random integration and drug selection, this method allows bona fide isogenic settings for high-throughput functional genomics, proteomics, and regulatory DNA analysis in essentially any transformed human cell type and in primary cells.
Collapse
Affiliation(s)
- Russell C DeKelver
- Sangamo BioSciences, Inc., Point Richmond Tech Center, Richmond, California 94804, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Labov JB, Reid AH, Yamamoto KR. Integrated biology and undergraduate science education: a new biology education for the twenty-first century? CBE Life Sci Educ 2010; 9:10-6. [PMID: 20194802 PMCID: PMC2830155 DOI: 10.1187/cbe.09-12-0092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Jay B Labov
- Center for Education National Research Council, Washington, DC 20001, USA.
| | | | | |
Collapse
|
29
|
Beck IME, Vanden Berghe W, Vermeulen L, Yamamoto KR, Haegeman G, De Bosscher K. Crosstalk in inflammation: the interplay of glucocorticoid receptor-based mechanisms and kinases and phosphatases. Endocr Rev 2009; 30:830-82. [PMID: 19890091 PMCID: PMC2818158 DOI: 10.1210/er.2009-0013] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 08/18/2009] [Indexed: 12/20/2022]
Abstract
Glucocorticoids (GCs) are steroidal ligands for the GC receptor (GR), which can function as a ligand-activated transcription factor. These steroidal ligands and derivatives thereof are the first line of treatment in a vast array of inflammatory diseases. However, due to the general surge of side effects associated with long-term use of GCs and the potential problem of GC resistance in some patients, the scientific world continues to search for a better understanding of the GC-mediated antiinflammatory mechanisms. The reversible phosphomodification of various mediators in the inflammatory process plays a key role in modulating and fine-tuning the sensitivity, longevity, and intensity of the inflammatory response. As such, the antiinflammatory GCs can modulate the activity and/or expression of various kinases and phosphatases, thus affecting the signaling efficacy toward the propagation of proinflammatory gene expression and proinflammatory gene mRNA stability. Conversely, phosphorylation of GR can affect GR ligand- and DNA-binding affinity, mobility, and cofactor recruitment, culminating in altered transactivation and transrepression capabilities of GR, and consequently leading to a modified antiinflammatory potential. Recently, new roles for kinases and phosphatases have been described in GR-based antiinflammatory mechanisms. Moreover, kinase inhibitors have become increasingly important as antiinflammatory tools, not only for research but also for therapeutic purposes. In light of these developments, we aim to illuminate the integrated interplay between GR signaling and its correlating kinases and phosphatases in the context of the clinically important combat of inflammation, giving attention to implications on GC-mediated side effects and therapy resistance.
Collapse
Affiliation(s)
- Ilse M E Beck
- Laboratory of Eukaryotic Gene Expression and Signal Transduction, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | | | | | | | | | | |
Collapse
|
30
|
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 2009; 324:407-10. [PMID: 19372434 DOI: 10.1126/science.1164265] [Citation(s) in RCA: 506] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genes are not simply turned on or off, but instead their expression is fine-tuned to meet the needs of a cell. How genes are modulated so precisely is not well understood. The glucocorticoid receptor (GR) regulates target genes by associating with specific DNA binding sites, the sequences of which differ between genes. Traditionally, these binding sites have been viewed only as docking sites. Using structural, biochemical, and cell-based assays, we show that GR binding sequences, differing by as little as a single base pair, differentially affect GR conformation and regulatory activity. We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes.
Collapse
Affiliation(s)
- Sebastiaan H Meijsing
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | | | | | | | | | | |
Collapse
|
31
|
Abstract
Differentiation of 3T3-L1 preadipocytes can be induced by a 2-d treatment with a factor "cocktail" (DIM) containing the synthetic glucocorticoid dexamethasone (dex), insulin, the phosphodiesterase inhibitor methylisobutylxanthine (IBMX) and fetal bovine serum (FBS). We temporally uncoupled the activities of the four DIM components and found that treatment with dex for 48 h followed by IBMX treatment for 48 h was sufficient for adipogenesis, whereas treatment with IBMX followed by dex failed to induce significant differentiation. Similar results were obtained with C3H10T1/2 and primary mesenchymal stem cells. The 3T3-L1 adipocytes differentiated by sequential treatment with dex and IBMX displayed insulin sensitivity equivalent to DIM adipocytes, but had lower sensitivity to ISO-stimulated lipolysis and reduced triglyceride content. The nondifferentiating IBMX-then-dex treatment produced transient expression of adipogenic transcriptional regulatory factors C/EBPbeta and C/EBPdelta, and little induction of terminal differentiation factors C/EBPalpha and PPARgamma. Moreover, the adipogenesis inhibitor preadipocyte factor-1 (Pref-1) was repressed by DIM or by dex-then-IBMX, but not by IBMX-then-dex treatment. We conclude that glucocorticoids drive preadipocytes to a novel intermediate cellular state, the dex-primed preadipocyte, during adipogenesis in cell culture, and that Pref-1 repression may be a cell fate determinant in preadipocytes.
Collapse
Affiliation(s)
- Carlos Pantoja
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94107-2280, USA
| | | | | |
Collapse
|
32
|
Taubert S, Hansen M, Van Gilst MR, Cooper SB, Yamamoto KR. The Mediator subunit MDT-15 confers metabolic adaptation to ingested material. PLoS Genet 2008; 4:e1000021. [PMID: 18454197 PMCID: PMC2265483 DOI: 10.1371/journal.pgen.1000021] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 01/10/2008] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, RNA polymerase II (PolII) dependent gene expression requires accessory factors termed transcriptional coregulators. One coregulator that universally contributes to PolII-dependent transcription is the Mediator, a multisubunit complex that is targeted by many transcriptional regulatory factors. For example, the Caenorhabditis elegans Mediator subunit MDT-15 confers the regulatory actions of the sterol response element binding protein SBP-1 and the nuclear hormone receptor NHR-49 on fatty acid metabolism. Here, we demonstrate that MDT-15 displays a broader spectrum of activities, and that it integrates metabolic responses to materials ingested by C. elegans. Depletion of MDT-15 protein or mutation of the mdt-15 gene abrogated induction of specific detoxification genes in response to certain xenobiotics or heavy metals, rendering these animals hypersensitive to toxin exposure. Intriguingly, MDT-15 appeared to selectively affect stress responses related to ingestion, as MDT-15 functional defects did not abrogate other stress responses, e.g., thermotolerance. Together with our previous finding that MDT-15:NHR-49 regulatory complexes coordinate a sector of the fasting response, we propose a model whereby MDT-15 integrates several transcriptional regulatory pathways to monitor both the availability and quality of ingested materials, including nutrients and xenobiotic compounds. All organisms adapt their physiology to external input, such as altered food availability or toxic challenges. Many of these responses are driven by changes in gene transcription. In general, sequence specific DNA-binding regulatory factors are considered the specificity determinants of the transcriptional output. Here, we show that, in the roundworm Caenorhabditis elegans, one subunit of a >20 subunit, evolutionarily conserved, non-DNA binding co-factor termed Mediator, specifies a portion of the metabolic responses to a mixture of ingested material. This protein, MDT-15, is required for appropriate expression of genes that protect worms from the effects of toxic compounds and heavy metals. Our previous findings showed that the same protein also cooperates with other regulators to coordinate lipid metabolism. We suggest that MDT-15 may “route” transcriptional responses appropriate to the ingested material. This physiological scope appears broader and more sophisticated than that of any individual regulatory factor, thus coordinating systemic metabolic adaptation with ingestion. Given the evolutionary conservation of MDT-15 and the Mediator, a similar regulatory pathway may ensure health and longevity in mammals.
Collapse
Affiliation(s)
- Stefan Taubert
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Malene Hansen
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Marc R. Van Gilst
- Fred Hutchinson Cancer Research Center, Basic Sciences Division, Seattle, Washington, United States of America
| | - Samantha B. Cooper
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program of Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
33
|
Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci U S A 2007; 104:15858-63. [PMID: 17898169 PMCID: PMC2000427 DOI: 10.1073/pnas.0707413104] [Citation(s) in RCA: 637] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Airway inflammation and epithelial remodeling are two key features of asthma. IL-13 and other cytokines produced during T helper type 2 cell-driven allergic inflammation contribute to airway epithelial goblet cell metaplasia and may alter epithelial-mesenchymal signaling, leading to increased subepithelial fibrosis or hyperplasia of smooth muscle. The beneficial effects of corticosteroids in asthma could relate to their ability to directly or indirectly decrease epithelial cell activation by inflammatory cells and cytokines. To identify markers of epithelial cell dysfunction and the effects of corticosteroids on epithelial cells in asthma, we studied airway epithelial cells collected from asthmatic subjects enrolled in a randomized controlled trial of inhaled corticosteroids, from healthy subjects and from smokers (disease control). By using gene expression microarrays, we found that chloride channel, calcium-activated, family member 1 (CLCA1), periostin, and serine peptidase inhibitor, clade B (ovalbumin), member 2 (serpinB2) were up-regulated in asthma but not in smokers. Corticosteroid treatment down-regulated expression of these three genes and markedly up-regulated expression of FK506-binding protein 51 (FKBP51). Whereas high baseline expression of CLCA1, periostin, and serpinB2 was associated with a good clinical response to corticosteroids, high expression of FKBP51 was associated with a poor response. By using airway epithelial cells in culture, we found that IL-13 increased expression of CLCA1, periostin, and serpinB2, an effect that was suppressed by corticosteroids. Corticosteroids also induced expression of FKBP51. Taken together, our findings show that airway epithelial cells in asthma have a distinct activation profile and identify direct and cell-autonomous effects of corticosteroid treatment on airway epithelial cells that relate to treatment responses and can now be the focus of specific mechanistic studies.
Collapse
Affiliation(s)
- Prescott G. Woodruff
- *Division of Pulmonary and Critical Care Medicine and
- Cardiovascular Research Institute, and
| | - Homer A. Boushey
- *Division of Pulmonary and Critical Care Medicine and
- Cardiovascular Research Institute, and
| | | | | | - Yee Hwa Yang
- School of Mathematics and Statistics, University of Sydney, Sydney NSW 2006, Australia
| | | | | | | | | | - Carlos Pantoja
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
| | - David J. Erle
- *Division of Pulmonary and Critical Care Medicine and
- **Lung Biology Center, Department of Medicine
- Cardiovascular Research Institute, and
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
- To whom correspondence may be addressed at:
University of California at San Francisco, Box 2280, Genentech Hall S572D, 600 16th Street, San Francisco, CA 94158-2517. E-mail:
| | - John V. Fahy
- *Division of Pulmonary and Critical Care Medicine and
- Cardiovascular Research Institute, and
- To whom correspondence may be addressed at:
University of California at San Francisco, Box 0130, 505 Parnassus Avenue, San Francisco, CA 94143. E-mail:
| |
Collapse
|
34
|
So AYL, Chaivorapol C, Bolton EC, Li H, Yamamoto KR. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet 2007; 3:e94. [PMID: 17559307 PMCID: PMC1904358 DOI: 10.1371/journal.pgen.0030094] [Citation(s) in RCA: 240] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/23/2007] [Indexed: 11/19/2022] Open
Abstract
The glucocorticoid receptor (GR) associates with glucocorticoid response elements (GREs) and regulates selective gene transcription in a cell-specific manner. Native GREs are typically thought to be composite elements that recruit GR as well as other regulatory factors into functional complexes. We assessed whether GR occupancy is commonly a limiting determinant of GRE function as well as the extent to which core GR binding sequences and GRE architecture are conserved at functional loci. We surveyed 100-kb regions surrounding each of 548 known or potentially glucocorticoid-responsive genes in A549 human lung cells for GR-occupied GREs. We found that GR was bound in A549 cells predominately near genes responsive to glucocorticoids in those cells and not at genes regulated by GR in other cells. The GREs were positionally conserved at each responsive gene but across the set of responsive genes were distributed equally upstream and downstream of the transcription start sites, with 63% of them >10 kb from those sites. Strikingly, although the core GR binding sequences across the set of GREs varied extensively around a consensus, the precise sequence at an individual GRE was conserved across four mammalian species. Similarly, sequences flanking the core GR binding sites also varied among GREs but were conserved at individual GREs. We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information. The glucocorticoid receptor (GR) regulates a myriad of physiological functions, such as cell differentiation and metabolism, achieved through modulating transcription in a cell- and gene-specific manner. However, the determinants that specify cell- and gene-specific GR transcriptional regulation are not well established. We describe three properties that contribute to this specificity: (1) GR occupancy at genomic glucocorticoid response elements (GREs) appears to be a primary determinant of glucocorticoid responsiveness; (2) the DNA sequences bound by GR vary widely around a consensus, but the precise sequences of individual GREs are highly conserved, suggesting a role for these sequences in gene-specific GR transcriptional regulation; and (3) native chromosomal GREs were generally found to be composite elements, comprised of multiple factor binding sites that were highly variable in composition, but as with the GR binding sequences, highly conserved at individual GREs. In addition, we discovered that most GREs were positioned far from their GR target genes and that they were equally distributed upstream and downstream of the target genes. These findings, which may be applicable to other regulatory factors, provide fundamental insights for understanding cell- and gene-specific transcriptional regulation.
Collapse
Affiliation(s)
- Alex Yick-Lun So
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Christina Chaivorapol
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
| | - Eric C Bolton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
35
|
Bolton EC, So AY, Chaivorapol C, Haqq CM, Li H, Yamamoto KR. Cell- and gene-specific regulation of primary target genes by the androgen receptor. Genes Dev 2007; 21:2005-17. [PMID: 17699749 PMCID: PMC1948856 DOI: 10.1101/gad.1564207] [Citation(s) in RCA: 279] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 07/06/2007] [Indexed: 01/08/2023]
Abstract
The androgen receptor (AR) mediates the physiologic and pathophysiologic effects of androgens including sexual differentiation, prostate development, and cancer progression by binding to genomic androgen response elements (AREs), which influence transcription of AR target genes. The composition and context of AREs differ between genes, thus enabling AR to confer multiple regulatory functions within a single nucleus. We used expression profiling of an immortalized human prostate epithelial cell line to identify 205 androgen-responsive genes (ARGs), most of them novel. In addition, we performed chromatin immunoprecipitation to identify 524 AR binding regions and validated in reporter assays the ARE activities of several such regions. Interestingly, 67% of our AREs resided within approximately 50 kb of the transcription start sites of 84% of our ARGs. Indeed, most ARGs were associated with two or more AREs, and ARGs were sometimes themselves linked in gene clusters containing up to 13 AREs and 12 ARGs. AREs appeared typically to be composite elements, containing AR binding sequences adjacent to binding motifs for other transcriptional regulators. Functionally, ARGs were commonly involved in prostate cell proliferation, communication, differentiation, and possibly cancer progression. Our results provide new insights into cell- and gene-specific mechanisms of transcriptional regulation of androgen-responsive gene networks.
Collapse
Affiliation(s)
- Eric C. Bolton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
| | - Alex Y. So
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, USA
| | - Christina Chaivorapol
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143, USA
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, California 94143, USA
| | - Christopher M. Haqq
- Department of Urology, University of California, San Francisco, California 94143, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143, USA
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, California 94143, USA
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, USA
| |
Collapse
|
36
|
Ricketson D, Hostick U, Fang L, Yamamoto KR, Darimont BD. A conformational switch in the ligand-binding domain regulates the dependence of the glucocorticoid receptor on Hsp90. J Mol Biol 2007; 368:729-41. [PMID: 17367809 PMCID: PMC2596751 DOI: 10.1016/j.jmb.2007.02.057] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 02/07/2007] [Accepted: 02/08/2007] [Indexed: 01/21/2023]
Abstract
Steroid hormone receptors (SRs) are transcription factors that act as regulatory switches by altering gene expression in response to ligands. The highly conserved ligand-binding domain of SRs is a precise but versatile molecular switch that can adopt distinct conformations. Differential stabilization of these conformations by ligands, DNA response elements and transcriptional coregulators controls the activity of SRs in a gene-specific and cell-specific manner. In the case of the glucocorticoid receptor (GR), high-affinity ligand binding requires the interaction of the LBD with the heat shock protein 90 (Hsp90). Here, we show that the dependence of the ligand binding ability of GR on Hsp90 can be modified by the replacement of single amino acids within an allosteric network that connects the buried ligand-binding pocket and a solvent-exposed coregulator interaction surface. Each of the identified mutations altered the equilibrium between alternative GR conformations distinctively, indicating that the Hsp90 dependence of SRs may correlate with differences in the conformational dynamics of these receptors. Our results suggest that Hsp90 stabilizes the GR ligand-binding pocket indirectly by utilizing the allosteric network, while allowing the receptor to remain structurally uncommitted. Thus, in addition to ensuring the accessibility of the GR ligand-binding pocket to ligands, Hsp90 seems to enable hormones and coregulators to act as allosteric effectors, which forms the basis for gene-specific and cell-specific responses of GR to ligands.
Collapse
Affiliation(s)
- D Ricketson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1229, USA
| | | | | | | | | |
Collapse
|
37
|
Meijsing SH, Elbi C, Luecke HF, Hager GL, Yamamoto KR. The ligand binding domain controls glucocorticoid receptor dynamics independent of ligand release. Mol Cell Biol 2007; 27:2442-51. [PMID: 17261597 PMCID: PMC1899895 DOI: 10.1128/mcb.01570-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ligand binding to the glucocorticoid receptor (GR) results in receptor binding to glucocorticoid response elements (GREs) and the formation of transcriptional regulatory complexes. Equally important, these complexes are continuously disassembled, with active processes driving GR off GREs. We found that co-chaperone p23-dependent disruption of GR-driven transcription depended on the ligand binding domain (LBD). Next, we examined the importance of the LBD and of ligand dissociation in GR-GRE dissociation in living cells. We showed in fluorescence recovery after photobleaching studies that dissociation of GR from GREs is faster in the absence of the LBD. Furthermore, GR interaction with a target promoter revealed ligand-specific exchange rates. However, using covalently binding ligands, we demonstrated that ligand dissociation is not required for receptor dissociation from GREs. Overall, these studies showed that activities impinging on the LBD regulate GR exchange with GREs but that the dissociation of GR from GREs is independent from ligand dissociation.
Collapse
Affiliation(s)
- Sebastiaan H Meijsing
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, 600 16th Street, Room GH-S574, San Francisco, CA 94107-2280, USA
| | | | | | | | | |
Collapse
|
38
|
Abstract
A pluripotent cell line, C3H10T1/2, is induced to undergo adipogenesis by a mixture of factors that includes a glucocorticoid such as dexamethasone. We found that expression of myostatin (MSTN), a TGF-beta family member extensively studied in muscle, was induced by dexamethasone under those differentiation conditions. Moreover, MSTN could substitute for dexamethasone in the adipogenesis mixture. However, the adipocytes induced by MSTN in both cell culture and transgenic mice were small and expressed markers characteristic of immature adipocytes. These adipocytes exhibited cell-autonomous increases in insulin sensitivity and glucose oxidation. In mice, these effects produced elevated systemic insulin sensitivity and resistance to diet-induced obesity. Modulation of the final stages of adipogenesis may provide a novel approach to understanding and treating metabolic disease.
Collapse
Affiliation(s)
| | - Ryan S. Streeper
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94143
| | - Robert V. Farese
- Medicine, and
- Biochemistry and Biophysics, University of California, San Francisco, CA 94143; and
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94143
| | | |
Collapse
|
39
|
Taubert S, Van Gilst MR, Hansen M, Yamamoto KR. A Mediator subunit, MDT-15, integrates regulation of fatty acid metabolism by NHR-49-dependent and -independent pathways in C. elegans. Genes Dev 2006; 20:1137-49. [PMID: 16651656 PMCID: PMC1472473 DOI: 10.1101/gad.1395406] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Caenorhabditis elegans Nuclear Hormone Receptor NHR-49 coordinates expression of fatty acid (FA) metabolic genes during periods of feeding and in response to fasting. Here we report the identification of MDT-15, a subunit of the C. elegans Mediator complex, as an NHR-49-interacting protein and transcriptional coactivator. Knockdown of mdt-15 by RNA interference (RNAi) prevented fasting-induced mRNA accumulation of NHR-49 targets in vivo, and fasting-independent expression of other NHR-49 target genes, including two FA-Delta9-desaturases (fat-5, fat-7). Interestingly, mdt-15 RNAi affected additional FA-metabolism genes (including the third FA-Delta9-desaturase, fat-6) that are regulated independently of NHR-49, suggesting that distinct unidentified regulatory factors also recruit MDT-15 to selectively modulate metabolic gene expression. The deregulation of FA-Delta9-desaturases by knockdown of mdt-15 correlated with dramatically decreased levels of unsaturated FAs and multiple deleterious phenotypes (short life span, sterility, uncoordinated locomotion, and morphological defects). Importantly, dietary addition of specific polyunsaturated FAs partially suppressed these pleiotropic phenotypes. Thus, failure to properly govern FA-Delta9-desaturation contributed to decreased nematode viability. Our findings imply that a single subunit of the Mediator complex, MDT-15, integrates the activities of several distinct regulatory factors to coordinate metabolic and hormonal regulation of FA metabolism.
Collapse
Affiliation(s)
- Stefan Taubert
- Department of Cellular and Molecular Pharmacology, University of California, San Francicso, CA 94143, USA
| | | | | | | |
Collapse
|
40
|
Wang JC, Shah N, Pantoja C, Meijsing SH, Ho JD, Scanlan TS, Yamamoto KR. Novel arylpyrazole compounds selectively modulate glucocorticoid receptor regulatory activity. Genes Dev 2006; 20:689-99. [PMID: 16543221 PMCID: PMC1413289 DOI: 10.1101/gad.1400506] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The activities of intracellular receptors are regulated by their cognate ligands. Here we show that a series of related arylpyrazole compounds, which specifically bind the glucocorticoid receptor (GR), selectively modulated GR-regulated biological functions in preadipocyte, pre-osteoblast, and lung epithelial cell lines. Indeed, when we monitored 17 endogenous GR target genes in one of these cell types, we found that distinct arylpyrazole compounds induced different expression patterns. We showed by chromatin immunoprecipitation that the arylpyrazole compounds regulated, in a gene-specific manner, either GR occupancy of the genomic glucocorticoid response element (GRE) or events after GR association, such as histone modification. Overall, our results establish that subtle differences in ligand chemistry can profoundly influence the transcriptional regulatory activity of GR, and that endogenous genes bearing natural GREs are especially sensitive detectors of these differences.
Collapse
Affiliation(s)
- Jen-Chywan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94107-2280, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
Lo B, Zettler P, Cedars MI, Gates E, Kriegstein AR, Oberman M, Reijo Pera R, Wagner RM, Wuerth MT, Wolf LE, Yamamoto KR. Translational research: toward better characterization of human embryonic stem cell lines. Stem Cells 2006; 23:1454-9. [PMID: 16293581 DOI: 10.1634/stemcells.2005-ed.4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Scientific progress in human embryonic stem cell (hESC) research and increased funding make it imperative to look ahead to the ethical issues generated by the expected use of hESCs for transplantation. Several issues should be addressed now, even though phase I clinical trials of hESC transplantation are still in the future. To minimize the risk of hESC transplantation, donors of materials used to derive hESC lines will need to be recontacted to update their medical history and screening. Because of privacy concerns, such recontact needs to be discussed and agreed to at the time of donation, before new hESC lines are derived. Informed consent for phase I clinical trials of hESC transplantation also raises ethical concerns. In previous phase I trials of highly innovative interventions, allegations that trial participants had not really understood the risk and benefits caused delays in subsequent trials. Thus, researchers should consider what information needs to be discussed during the consent process for hESC clinical trials and how to verify that participants have a realistic understanding of the study. Lack of attention to the special ethical concerns raised by clinical trials of hESC transplantation and their implications for the derivation of new hESC lines may undermine or delay progress toward stem cell therapies.
Collapse
Affiliation(s)
- Bernard Lo
- Program in Medical Ethics and Division of General Internal Medicine, University of California San Francisco, San Francisco, California, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Van Gilst MR, Hadjivassiliou H, Yamamoto KR. A Caenorhabditis elegans nutrient response system partially dependent on nuclear receptor NHR-49. Proc Natl Acad Sci U S A 2005; 102:13496-501. [PMID: 16157872 PMCID: PMC1201344 DOI: 10.1073/pnas.0506234102] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Appropriate response to nutritional stress is critical for animal survival and metabolic health. To better understand regulatory networks that sense and respond to nutritional availability, we developed a quantitative RT-PCR strategy to monitor changes in metabolic gene expression resulting from short-term food deprivation (fasting) in Caenorhabditis elegans. Examining 97 fat and glucose metabolism genes in fed and fasted animals, we identified 18 genes significantly influenced by food withdrawal in all developmental stages. Fasting response genes fell into multiple kinetic classes, with some genes showing significant activation or repression just 1 h after food was removed. As expected, fasting stimulated the expression of genes involved in mobilizing fats for energy production, including mitochondrial beta-oxidation genes. Surprisingly, however, we found that other mitochondrial beta-oxidation genes were repressed by food deprivation. Fasting also affected genes involved in mono- and polyunsaturated fatty acid synthesis: four desaturases were induced, and one stearoyl-CoA desaturase (SCD) was strongly repressed. Accordingly, fasted animals displayed considerable changes in fatty acid composition. Finally, nuclear receptor nhr-49 played a key role in nutritional response, enabling induction of beta-oxidation genes upon food deprivation and facilitating activation of SCD in fed animals. Our characterization of a fasting response system and our finding that nhr-49 regulates a sector within this system provide insight into the mechanisms by which animals respond to nutritional signals.
Collapse
Affiliation(s)
- Marc R Van Gilst
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-2280, USA
| | | | | |
Collapse
|
43
|
Luecke HF, Yamamoto KR. The glucocorticoid receptor blocks P-TEFb recruitment by NFkappaB to effect promoter-specific transcriptional repression. Genes Dev 2005; 19:1116-27. [PMID: 15879558 PMCID: PMC1091745 DOI: 10.1101/gad.1297105] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To investigate the determinants of promoter-specific gene regulation by the glucocorticoid receptor (GR), we compared the composition and function of regulatory complexes at two NFkappaB-responsive genes that are differentially regulated by GR. Transcription of the IL-8 and IkappaBalpha genes is stimulated by TNFalpha in A549 cells, but GR selectively represses IL-8 mRNA synthesis by inhibiting Ser2 phosphorylation of the RNA polymerase II (pol II) C-terminal domain (CTD). The proximal kappaB elements at these genes differ in sequence by a single base pair, and both recruited RelA and p50. Surprisingly, GR was recruited to both of these elements, despite the fact that GR failed to repress the IkappaBalpha promoter. Rather, the regulatory complexes formed at IL-8 and IkappaBalpha were distinguished by differential recruitment of the Ser2 CTD kinase, P-TEFb. Disruption of P-TEFb function by the Cdk-inhibitor, DRB, or by small interfering RNA selectively blocked TNFalpha stimulation of IL-8 mRNA production. GR competed with P-TEFb recruitment to the IL-8 promoter. Strikingly, IL-8 mRNA synthesis was repressed by GR at a post-initiation step, demonstrating that promoter proximal regulatory sequences assemble complexes that impact early and late stages of mRNA synthesis. Thus, GR accomplishes selective repression by targeting promoter-specific components of NFkappaB regulatory complexes.
Collapse
Affiliation(s)
- Hans F Luecke
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94107-2280, USA
| | | |
Collapse
|
44
|
Shostak Y, Yamamoto KR. Overlapping but separable determinants of DNA binding and nuclear localization map to the C-terminal end of the Caenorhabditis elegans DAF-12 DNA binding domain. J Biol Chem 2005; 280:6554-60. [PMID: 15611047 DOI: 10.1074/jbc.m412928200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins are commonly viewed as modular assemblies of functional domains. We analyzed a loss-of-function mutation in the Caenorhabditis elegans intracellular receptor DAF-12, a conservative substitution of an arginine to a lysine at position 197 (R197K). Arg(197) resides in region similar to a nuclear localization signal, just downstream of the receptor minimal zinc finger DNA binding domain (DBD) core. We found that the R197K, but not mutations of neighboring arginine or lysine residues, dramatically reduced DAF-12 transcriptional regulatory activity in a yeast reporter assay. This reduction in regulatory activity correlated with greatly decreased DNA binding affinity in vitro, suggesting a role for the DAF-12 DBD C-terminal region (dbdC), and specifically for Arg(197), in DNA binding. Remarkably, three basic residues immediately contiguous with Arg(197) played little role in DNA binding and rather affected nuclear localization; in contrast, Arg(197) itself was dispensable for nuclear localization. Thus, DAF-12 dbdC harbors overlapping but separable determinants of DNA binding and nuclear localization in a single small region.
Collapse
Affiliation(s)
- Yuriy Shostak
- Program in Biochemistry and Molecular Biology and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-2280
| | | |
Collapse
|
45
|
Gilst MRV, Hadjivassiliou H, Jolly A, Yamamoto KR. Nuclear hormone receptor NHR-49 controls fat consumption and fatty acid composition in C. elegans. PLoS Biol 2005; 3:e53. [PMID: 15719061 PMCID: PMC547972 DOI: 10.1371/journal.pbio.0030053] [Citation(s) in RCA: 297] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 12/07/2004] [Indexed: 11/19/2022] Open
Abstract
Mammalian nuclear hormone receptors (NHRs), such as liver X receptor, farnesoid X receptor, and peroxisome proliferator-activated receptors (PPARs), precisely control energy metabolism. Consequently, these receptors are important targets for the treatment of metabolic diseases, including diabetes and obesity. A thorough understanding of NHR fat regulatory networks has been limited, however, by a lack of genetically tractable experimental systems. Here we show that deletion of the Caenorhabditis elegans NHR gene nhr-49 yielded worms with elevated fat content and shortened life span. Employing a quantitative RT-PCR screen, we found that nhr-49 influenced the expression of 13 genes involved in energy metabolism. Indeed, nhr-49 served as a key regulator of fat usage, modulating pathways that control the consumption of fat and maintain a normal balance of fatty acid saturation. We found that the two phenotypes of the nhr-49 knockout were linked to distinct pathways and were separable: The high-fat phenotype was due to reduced expression of enzymes in fatty acid beta-oxidation, and the shortened adult life span resulted from impaired expression of a stearoyl-CoA desaturase. Despite its sequence relationship with the mammalian hepatocyte nuclear factor 4 receptor, the biological activities of nhr-49 were most similar to those of the mammalian PPARs, implying an evolutionarily conserved role for NHRs in modulating fat consumption and composition. Our findings in C. elegans provide novel insights into how NHR regulatory networks are coordinated to govern fat metabolism.
Collapse
Affiliation(s)
- Marc R. Van Gilst
- 1Department of Cellular and Molecular Pharmacology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Haralambos Hadjivassiliou
- 1Department of Cellular and Molecular Pharmacology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Amber Jolly
- 1Department of Cellular and Molecular Pharmacology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Keith R Yamamoto
- 1Department of Cellular and Molecular Pharmacology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| |
Collapse
|
46
|
Abstract
Intracellular receptor DAF-12 regulates dauer formation and developmental age and affects Caenorhabditis elegans lifespan. Genetic analyses place DAF-12 at the convergence of several signal transduction pathways; however, the downstream effectors and the molecular basis for the receptor's multiple physiological outputs are unknown. Beginning with C. elegans genomic DNA, we devised a procedure for multiple rounds of selection and amplification that yielded fragments bearing DAF-12-binding sites. These genomic fragments mediated DAF-12-dependent transcriptional regulation both in Saccharomyces cerevisiae and in C. elegans; that is, they served as functional DAF-12 response elements. We determined that most of the genomic fragments that displayed DAF-12 response element activity in yeast were linked to genes that were regulated by DAF-12 in C. elegans; indeed, the response element-containing fragments typically resided within clusters of DAF-12-regulated genes. DAF-12 target gene regulation was developmental program and stage specific, potentially predicting a fit of these targets into regulatory networks governing aspects of C. elegans reproductive development and dauer formation.
Collapse
Affiliation(s)
- Yuriy Shostak
- Program in Biochemistry and Molecular Biology, University of California, San Francisco, California 94143-2280, USA
| | | | | | | |
Collapse
|
47
|
Wang JC, Derynck MK, Nonaka DF, Khodabakhsh DB, Haqq C, Yamamoto KR. Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes. Proc Natl Acad Sci U S A 2004; 101:15603-8. [PMID: 15501915 PMCID: PMC524211 DOI: 10.1073/pnas.0407008101] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The global physiological effects of glucocorticoids are well established, and the framework of transcriptional regulation by the glucocorticoid receptor (GR) has been described. However, the genes directly under GR control that trigger these physiological effects are largely unknown. To address this issue in a single cell type, we identified glucocorticoid-responsive genes in A549 human lung adenocarcinoma cells by microarray analysis and quantitative real-time PCR. Reduction of GR expression by RNA interference diminished the effects of dexamethasone on all tested target genes, thus confirming the essential role of GR in glucocorticoid-regulated gene expression. To identify primary GR target genes, in which GR is a component of the transcriptional regulatory complex, we developed a strategy that uses chromatin immunoprecipitation to scan putative regulatory regions of target genes for sites occupied by specifically bound GR. We screened 11 glucocorticoid-regulated genes, and we identified GR-binding regions for eight of them (five induced and three repressed). Thus, our approach provides a means for rapid identification of primary GR target genes and glucocorticoid-response elements, which will facilitate analyses of transcriptional regulatory mechanisms and determination of hormone-regulated gene networks.
Collapse
Affiliation(s)
- Jen-Chywan Wang
- Departments of Cellular and Molecular Pharmacology and Medicine, University of California-San Francisco, S572D, Genentech Hall, 600 16th Street, San Francisco, CA 94107-2280, USA
| | | | | | | | | | | |
Collapse
|
48
|
Affiliation(s)
- Keith R Yamamoto
- School of Medicine and the Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| |
Collapse
|
49
|
Lo B, Chou V, Cedars MI, Gates E, Taylor RN, Wagner RM, Wolf L, Yamamoto KR. Informed consent in human oocyte, embryo, and embryonic stem cell research. Fertil Steril 2004; 82:559-63. [PMID: 15374695 DOI: 10.1016/j.fertnstert.2004.01.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 01/21/2004] [Accepted: 01/21/2004] [Indexed: 10/26/2022]
Abstract
Research with human oocytes, embryos, and additional embryonic stem cell lines is needed to address important scientific questions and to fulfill the promise of stem cell transplantation for degenerative diseases. Proponents need to develop guidelines for the appropriate conduct of embryonic stem cell research. Such guidelines will help build public trust and acceptance for this research. In this article, we offer recommendations for informed consent, discussing who should give consent, what the consent process should cover, when consent should be obtained, and who should obtain consent. Consent to use embryos for research should be obtained from oocyte and sperm donors as well as from the woman or couple undergoing infertility treatment. The consent discussion must cover information that donors need to know to make an informed decision about various types of research. Donations for research should be discussed at the initiation of advanced infertility treatment and reconfirmed if possible at the time of actual donation for research. Treating assisted reproduction technology physicians can help with the consent process, provided that they are not involved in the research.
Collapse
Affiliation(s)
- Bernard Lo
- Program in Medical Ethics and the Division of General Internal Medicine, Department of Medicine, University of California at San Francisco, 521 Parnassus Avenue, San Francisco, CA 94143-0903, USA.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Freedman ND, Yamamoto KR. Importin 7 and importin alpha/importin beta are nuclear import receptors for the glucocorticoid receptor. Mol Biol Cell 2004; 15:2276-86. [PMID: 15004228 PMCID: PMC404022 DOI: 10.1091/mbc.e03-11-0839] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 01/22/2004] [Accepted: 02/16/2004] [Indexed: 11/11/2022] Open
Abstract
The vertebrate glucocorticoid receptor (GR) is cytoplasmic without hormone and localizes to the nucleus after hormone binding. GR has two nuclear localization signals (NLS): NL1 is similar in sequence to the SV40 NLS; NL2 is poorly defined, residing in the ligand-binding domain. We found that GR displayed similar hormone-regulated compartmentalization in Saccharomyces cerevisiae and required the Sxm1 nuclear import receptor for NL2-mediated import. Two metazoan homologues of Sxm1, importin 7 and importin 8, bound both NL1 and NL2, whereas importin alpha selectively bound NL1. In an in vitro nuclear import assay, both importin 7 and the importin alpha-importin beta heterodimer could import a GR NL1 fragment. Under these conditions, full-length GR localized to nuclei in the presence but not absence of an unidentified component in cell extracts. Interestingly, importin 7, importin 8, and importin alpha bound GR even in the absence of hormone; thus, hormonal control of localization is exerted at a step downstream of import receptor binding.
Collapse
Affiliation(s)
- Neal D Freedman
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143-2280, USA
| | | |
Collapse
|