1
|
Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet 2024; 56:473-482. [PMID: 38361031 DOI: 10.1038/s41588-024-01658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
Collapse
Affiliation(s)
- Satoko Ishii
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taishi Kakizuka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Tagawa
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Chiaki Sanbo
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Miyanari
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
- Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
| |
Collapse
|
2
|
Abstract
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.
Collapse
Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
- Department of Physics, University of Maryland, College Park, Maryland, USA;
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland, USA;
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| |
Collapse
|
3
|
Ambwani S, Dolma R, Sharma R, Kaur A, Singh H, Ruj A, Ambwani TK. Modulation of inflammatory and oxidative stress biomarkers due to dexamethasone exposure in chicken splenocytes. Vet Immunol Immunopathol 2023; 262:110632. [PMID: 37517103 DOI: 10.1016/j.vetimm.2023.110632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Dexamethasone (DEXA) is a potent corticosteroid, commonly used for treating inflammatory, hypersensitive and allergic conditions. It is administered to birds with tumours. Many studies were conducted on its immunosuppressive effects; however none of the similar study is available employing chicken splenocytes culture system. The present study was conducted to assess DEXA induced alterations in inflammatory and oxidative stress biomarkers in chicken splenocytes due to its in vitro exposure. The maximum non-cytotoxic dose (MNCD) was evaluated and was further used for conducting lymphocytes proliferation assay (LPA), antioxidant assays (lipid peroxidation, GSH, superoxide dismutase and nitric oxide assays) and assessment of mRNA levels of various genes (IL-1β, IL-6, IL-10, LITAF, iNOS, NF-κB1, Nrf-2, Caspase-3 and -9) through qPCR. The MNCD was determined to be 30 ng/ml in chicken splenocytes culture system. DEXA caused reduction in B and T lymphocytes proliferation indicating its immunosuppressive effects, however improved the antioxidant status of the exposed splenocytes. The expression levels of IL-1β, IL-6, iNOS, LITAF and NF-κB1 were significantly reduced while IL-10 was enhanced, which signify potent anti-inflammatory potential of DEXA. NF-κB is a major transcription factor that regulates genes responsible for both, innate and adaptive immune responses and elicits inflammation. The nuclear factor erythroid 2-related factor 2 (Nrf-2) level was found to be up-regulated. Nrf-2 plays important role in combating the oxidant stress and its increased expression could be the reason of improved antioxidant status of DEXA exposed cells. Present findings indicated that DEXA exhibited modulation in anti-inflammatory, immunomodulatory and antioxidant mediators in chicken splenocytes.
Collapse
Affiliation(s)
- Sonu Ambwani
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India.
| | - Rigzin Dolma
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Raunak Sharma
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Amandip Kaur
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Himani Singh
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Anamitra Ruj
- Department of Molecular Biology and Genetic Engineering, C.B.S.H., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Tanuj Kumar Ambwani
- Department of Veterinary Physiology and Biochemistry, C.V.A.S., Govind Ballabh Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| |
Collapse
|
4
|
Borin C, Pieters T, Serafin V, Ntziachristos P. Emerging Epigenetic and Posttranslational Mechanisms Controlling Resistance to Glucocorticoids in Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e916. [PMID: 37359189 PMCID: PMC10289758 DOI: 10.1097/hs9.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Glucocorticoids are extensively used for the treatment of acute lymphoblastic leukemia as they pressure cancer cells to undergo apoptosis. Nevertheless, glucocorticoid partners, modifications, and mechanisms of action are hitherto poorly characterized. This hampers our understanding of therapy resistance, frequently occurring in leukemia despite the current therapeutic combinations using glucocorticoids in acute lymphoblastic leukemia. In this review, we initially cover the traditional view of glucocorticoid resistance and ways of targeting this resistance. We discuss recent progress in our understanding of chromatin and posttranslational properties of the glucocorticoid receptor that might be proven beneficial in our efforts to understand and target therapy resistance. We discuss emerging roles of pathways and proteins such as the lymphocyte-specific kinase that antagonizes glucocorticoid receptor activation and nuclear translocation. In addition, we provide an overview of ongoing therapeutic approaches that sensitize cells to glucocorticoids including small molecule inhibitors and proteolysis-targeting chimeras.
Collapse
Affiliation(s)
- Cristina Borin
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Valentina Serafin
- Department of Surgery Oncology and Gastroenterology, Oncology and Immunology Section, University of Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| |
Collapse
|
5
|
Angelov D, Boopathi R, Lone IN, Menoni H, Dimitrov S, Cadet J. Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking. Photochem Photobiol 2022; 99:296-312. [PMID: 35997098 DOI: 10.1111/php.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.
Collapse
Affiliation(s)
- Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Ramachandran Boopathi
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| |
Collapse
|
6
|
Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly. PLoS Genet 2022; 18:e1010277. [PMID: 35793348 PMCID: PMC9292117 DOI: 10.1371/journal.pgen.1010277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 07/18/2022] [Accepted: 05/28/2022] [Indexed: 12/01/2022] Open
Abstract
The nucleosome remodeling complexes (CRs) SWI/SNF, RSC, and Ino80C cooperate in evicting or repositioning nucleosomes to produce nucleosome depleted regions (NDRs) at the promoters of many yeast genes induced by amino acid starvation. We analyzed mutants depleted of the catalytic subunits of these CRs for binding of transcriptional activator Gcn4 and recruitment of TATA-binding protein (TBP) during preinitiation complex (PIC) assembly. RSC and Ino80 were found to enhance Gcn4 binding to both UAS elements in NDRs upstream of promoters and to unconventional binding sites within nucleosome-occupied coding sequences; and SWI/SNF contributes to UAS binding when RSC is depleted. All three CRs are actively recruited by Gcn4 to most UAS elements and appear to enhance Gcn4 binding by reducing nucleosome occupancies at the binding motifs, indicating a positive regulatory loop. SWI/SNF acts unexpectedly in WT cells to prevent excessive Gcn4 binding at many UAS elements, indicating a dual mode of action that is modulated by the presence of RSC. RSC and SWI/SNF collaborate to enhance TBP recruitment at Gcn4 target genes, together with Ino80C, in a manner associated with nucleosome eviction at the TBP binding sites. Cooperation among the CRs in TBP recruitment is also evident at the highly transcribed ribosomal protein genes, while RSC and Ino80C act more broadly than SWI/SNF at the majority of other constitutively expressed genes to stimulate this step in PIC assembly. Our findings indicate a complex interplay among the CRs in evicting promoter nucleosomes to regulate activator binding and stimulate PIC assembly. ATP-dependent chromatin remodelers (CRs), including SWI/SNF and RSC in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes, and we recently implicated the CR Ino80C in this process as well. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently via evicting nucleosomes from the Gcn4 binding motifs. At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. The CRs in turn are recruited by Gcn4, consistent with a positive feedback loop that enhances Gcn4 binding. The three CRs also cooperate to enhance TBP recruitment, again involving nucleosome depletion, at both Gcn4 target and highly expressed ribosomal protein genes, whereas only RSC and Ino80C act broadly throughout the genome to enhance this key step in preinitiation complex assembly. Our findings illuminate functional cooperation among multiple CRs in regulating activator binding and promoter activation.
Collapse
|
7
|
Strickland BA, Ansari SA, Dantoft W, Uhlenhaut NH. How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids. FEBS Lett 2022; 596:2596-2616. [PMID: 35612756 DOI: 10.1002/1873-3468.14409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/24/2022] [Accepted: 05/18/2022] [Indexed: 01/08/2023]
Abstract
Glucocorticoids (GCs) are widely used therapeutic agents to treat a broad range of inflammatory conditions. Their functional effects are elicited by binding to the glucocorticoid receptor (GR), which regulates transcription of distinct gene networks in response to ligand. However, the mechanisms governing various aspects of undesired side effects versus beneficial immunomodulation upon GR activation remain complex and incompletely understood. In this review, we discuss emerging models of inflammatory gene regulation by GR, highlighting GR's regulatory specificity conferred by context-dependent changes in chromatin architecture and transcription factor or co-regulator dynamics. GR controls both gene activation and repression, with the repression mechanism being central to favorable clinical outcomes. We describe current knowledge about 3D genome organization and its role in spatiotemporal transcriptional control by GR. Looking beyond, we summarize the evidence for dynamics in gene regulation by GR through cooperative convergence of epigenetic modifications, transcription factor crosstalk, molecular condensate formation and chromatin looping. Further characterizing these genomic events will reframe our understanding of mechanisms of transcriptional repression by GR.
Collapse
Affiliation(s)
- Benjamin A Strickland
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Suhail A Ansari
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Widad Dantoft
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - N Henriette Uhlenhaut
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| |
Collapse
|
8
|
Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022; 13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions induced by crosslinking agents such as formaldehyde (HCHO). Building artificial models to simulate the crosslinking process would advance our understanding of the underlying mechanisms and therefore develop coping strategies accordingly. Herein we report the design and synthesis of a Zn-based metal-organic framework with mixed ligands of 2,6-diaminopurine and amine-functionalized dicarboxylate, representing DNA and protein residues, respectively. Combined characterization techniques allow us to demonstrate the unusual efficiency of HCHO-crosslinking within the confined space of the titled MOF. Particularly, in situ single-crystal X-ray diffraction studies reveal a sequential methylene-knitting process upon HCHO addition, along with strong fluorescence that was not interfered with by other metabolites, glycine, and Tris. This work has successfully constructed a purine-based metal-organic framework with unoccupied Watson-Crick sites, serving as a crystalline model for HCHO-induced DPCs by mimicking the confinement effect of protein/DNA interactions.
Collapse
Affiliation(s)
- Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Xiao Xiong
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Yong-Liang Huang
- Department of Chemistry, Shantou University Medical College Shantou Guangdong 515041 P. R. China
| | - Mo Xie
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Weigang Lu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| |
Collapse
|
9
|
Varticovski L, Stavreva DA, McGowan A, Raziuddin R, Hager GL. Endocrine disruptors of sex hormone activities. Mol Cell Endocrinol 2022; 539:111415. [PMID: 34339825 PMCID: PMC8762672 DOI: 10.1016/j.mce.2021.111415] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022]
Abstract
Sex hormones, such as androgens, estrogens and progestins are naturally occurring compounds that tightly regulate endocrine systems in a variety of living organisms. Uncontrolled environmental exposure to these hormones or their biological and synthetic mimetics has been widely documented. Furthermore, water contaminants penetrate soil to affect flora, fauna and ultimately humans. Because endocrine systems evolved to respond to very small changes in hormone levels, the low levels found in the environment cannot be ignored. The combined actions of sex hormones with glucocorticoids and other nuclear receptors disruptors creates additional level of complexity including the newly described "dynamic assisted loading" mechanism. We reviewed the extensive literature pertaining to world-wide detection of these disruptors and created a detailed Table on the development and current status of methods used for their analysis.
Collapse
Affiliation(s)
- L Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - D A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A McGowan
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - R Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
10
|
Reb1, Cbf1, and Pho4 bias histone sliding and deposition away from their binding sites. Mol Cell Biol 2021; 42:e0047221. [PMID: 34898278 DOI: 10.1128/mcb.00472-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In transcriptionally active genes, nucleosome positions in promoters are regulated by nucleosome displacing factors (NDFs) and chromatin remodeling enzymes. Depletion of NDFs or the RSC chromatin remodeler shrinks or abolishes the nucleosome depleted regions (NDRs) in promoters, which can suppress gene activation and result in cryptic transcription. Despite their vital cellular functions, how the action of chromatin remodelers may be directly affected by site-specific binding factors like NDFs is poorly understood. Here we demonstrate that two NDFs, Reb1 and Cbf1, can direct both Chd1 and RSC chromatin remodeling enzymes in vitro, stimulating repositioning of the histone core away from their binding sites. Interestingly, although the Pho4 transcription factor had a much weaker effect on nucleosome positioning, both NDFs and Pho4 were able to similarly redirect positioning of hexasomes. In chaperone-mediated nucleosome assembly assays, Reb1 but not Pho4 showed an ability to block deposition of the histone H3/H4 tetramer, but Reb1 did not block addition of the H2A/H2B dimer to hexasomes. Our in vitro results show that NDFs bias the action of remodelers to increase the length of the free DNA in the vicinity of their binding sites. These results suggest that NDFs could directly affect NDR architecture through chromatin remodelers.
Collapse
|
11
|
Wang L, Oh TG, Magida J, Estepa G, Obayomi SMB, Chong LW, Gatchalian J, Yu RT, Atkins AR, Hargreaves D, Downes M, Wei Z, Evans RM. Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses by potentiating glucocorticoid receptor activity. Proc Natl Acad Sci U S A 2021; 118:e2109517118. [PMID: 34446564 PMCID: PMC8536317 DOI: 10.1073/pnas.2109517118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In macrophages, homeostatic and immune signals induce distinct sets of transcriptional responses, defining cellular identity and functional states. The activity of lineage-specific and signal-induced transcription factors are regulated by chromatin accessibility and other epigenetic modulators. Glucocorticoids are potent antiinflammatory drugs; however, the mechanisms by which they selectively attenuate inflammatory genes are not yet understood. Acting through the glucocorticoid receptor (GR), glucocorticoids directly repress inflammatory responses at transcriptional and epigenetic levels in macrophages. A major unanswered question relates to the sequence of events that result in the formation of repressive regions. In this study, we identify bromodomain containing 9 (BRD9), a component of SWI/SNF chromatin remodeling complex, as a modulator of glucocorticoid responses in macrophages. Inhibition, degradation, or genetic depletion of BRD9 in bone marrow-derived macrophages significantly attenuated their responses to both liposaccharides and interferon inflammatory stimuli. Notably, BRD9-regulated genes extensively overlap with those regulated by the synthetic glucocorticoid dexamethasone. Pharmacologic inhibition of BRD9 potentiated the antiinflammatory responses of dexamethasone, while the genetic deletion of BRD9 in macrophages reduced high-fat diet-induced adipose inflammation. Mechanistically, BRD9 colocalized at a subset of GR genomic binding sites, and depletion of BRD9 enhanced GR occupancy primarily at inflammatory-related genes to potentiate GR-induced repression. Collectively, these findings establish BRD9 as a genomic antagonist of GR at inflammatory-related genes in macrophages, and reveal a potential for BRD9 inhibitors to increase the therapeutic efficacies of glucocorticoids.
Collapse
Affiliation(s)
- Liu Wang
- Department of Physiology and Biomedical Engineering, Mayo Clinic Arizona, Scottsdale, AZ 85259
| | - Tae Gyu Oh
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Jason Magida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Gabriela Estepa
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - S M Bukola Obayomi
- Department of Physiology and Biomedical Engineering, Mayo Clinic Arizona, Scottsdale, AZ 85259
| | - Ling-Wa Chong
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Jovylyn Gatchalian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037
| | - Ruth T Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Annette R Atkins
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Diana Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;
| | - Zong Wei
- Department of Physiology and Biomedical Engineering, Mayo Clinic Arizona, Scottsdale, AZ 85259;
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;
| |
Collapse
|
12
|
Kumar R. Role of conformational dynamics and flexibilities in the steroid receptor-coregulator protein complex formation. Gen Comp Endocrinol 2021; 309:113780. [PMID: 33882296 DOI: 10.1016/j.ygcen.2021.113780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/21/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Understanding of the mechanisms of actions of the steroid hormone receptor (SHR)-coregulator (CoR) protein complexes in the gene regulations has revolutionized the field of molecular endocrinology and endocrine-related oncology. The discovery and characterization of steroid receptor coactivators (SRCs) and their ability to bind various transcription factors including SHRs to coordinate the regulation of multiple target genes highlights their importance as key coregulators in various cellular signaling crosstalks as well as therapeutic target for various endocrine-related disorders specifically endocrine cancers. The dynamic nature of the SHR-CoR multi-protein complexes indicate the critical role of conformational flexibilities within specific protein(s). In recent years, the importance of conformational dynamics of the SHRs in the intramolecular and intermolecular allosteric regulations mediated via their intrinsically disordered (ID) surfaces has been highlighted. In this review article, we have discussed the importance of ID conformations within the SRCs that may also be playing an important role in the formation/deformation of multi protein complexes involving SHRs and CoRs and subsequent target gene regulation.
Collapse
Affiliation(s)
- Raj Kumar
- Department of Biomedical Sciences, University of Houston - College of Medicine, Houston, TX, United States.
| |
Collapse
|
13
|
Frank F, Liu X, Ortlund EA. Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation. Proc Natl Acad Sci U S A 2021; 118:e2024685118. [PMID: 34285072 PMCID: PMC8325269 DOI: 10.1073/pnas.2024685118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor (TF) that controls the tissue- and gene-specific transactivation and transrepression of thousands of target genes. Distinct GR DNA-binding sequences with activating or repressive activities have been identified, but how they modulate transcription in opposite ways is not known. We show that GR forms phase-separated condensates that specifically concentrate known coregulators via their intrinsically disordered regions (IDRs) in vitro. A combination of dynamic, multivalent (between IDRs) and specific, stable interactions (between LxxLL motifs and the GR ligand-binding domain) control the degree of recruitment. Importantly, GR DNA binding directs the selective partitioning of coregulators within GR condensates such that activating DNAs cause enhanced recruitment of coactivators. Our work shows that condensation controls GR function by modulating coregulator recruitment and provides a mechanism for the up- and down-regulation of GR target genes controlled by distinct DNA recognition elements.
Collapse
Affiliation(s)
- Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| |
Collapse
|
14
|
Benedetti R, Bajardi F, Capozziello S, Carafa V, Conte M, Del Sorbo MR, Nebbioso A, Singh M, Stunnenberg HG, Valadan M, Altucci L, Altucci C. Different Approaches to Unveil Biomolecule Configurations and Their Mutual Interactions. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1716241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- R. Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - F. Bajardi
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - S. Capozziello
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
- Gran Sasso Science Institute, L’Aquila, Italy
| | - V. Carafa
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Conte
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. R. Del Sorbo
- Istituto Statale d’Istruzione Superiore “Leonardo da Vinci”, Poggiomarino, NA, Italy
| | - A. Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Singh
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - H. G. Stunnenberg
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, the Netherlands
| | - M. Valadan
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - L. Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - C. Altucci
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| |
Collapse
|
15
|
Præstholm SM, Correia CM, Grøntved L. Multifaceted Control of GR Signaling and Its Impact on Hepatic Transcriptional Networks and Metabolism. Front Endocrinol (Lausanne) 2020; 11:572981. [PMID: 33133019 PMCID: PMC7578419 DOI: 10.3389/fendo.2020.572981] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Glucocorticoids (GCs) and the glucocorticoid receptor (GR) are important regulators of development, inflammation, stress response and metabolism, demonstrated in various diseases including Addison's disease, Cushing's syndrome and by the many side effects of prolonged clinical administration of GCs. These conditions include severe metabolic challenges in key metabolic organs like the liver. In the liver, GR is known to regulate the transcription of key enzymes in glucose and lipid metabolism and contribute to the regulation of circadian-expressed genes. Insights to the modes of GR regulation and the underlying functional mechanisms are key for understanding diseases and for the development of improved clinical uses of GCs. The activity and function of GR is regulated at numerous levels including ligand availability, interaction with heat shock protein (HSP) complexes, expression of GR isoforms and posttranslational modifications. Moreover, recent genomics studies show functional interaction with multiple transcription factors (TF) and coregulators in complex transcriptional networks controlling cell type-specific gene expression by GCs. In this review we describe the different regulatory steps important for GR activity and discuss how different TF interaction partners of GR selectively control hepatic gene transcription and metabolism.
Collapse
Affiliation(s)
| | | | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
16
|
Lightman SL, Birnie MT, Conway-Campbell BL. Dynamics of ACTH and Cortisol Secretion and Implications for Disease. Endocr Rev 2020; 41:bnaa002. [PMID: 32060528 PMCID: PMC7240781 DOI: 10.1210/endrev/bnaa002] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
The past decade has seen several critical advances in our understanding of hypothalamic-pituitary-adrenal (HPA) axis regulation. Homeostatic physiological circuits need to integrate multiple internal and external stimuli and provide a dynamic output appropriate for the response parameters of their target tissues. The HPA axis is an example of such a homeostatic system. Recent studies have shown that circadian rhythmicity of the major output of this system-the adrenal glucocorticoid hormones corticosterone in rodent and predominately cortisol in man-comprises varying amplitude pulses that exist due to a subhypothalamic pulse generator. Oscillating endogenous glucocorticoid signals interact with regulatory systems within individual parts of the axis including the adrenal gland itself, where a regulatory network can further modify the pulsatile release of hormone. The HPA axis output is in the form of a dynamic oscillating glucocorticoid signal that needs to be decoded at the cellular level. If the pulsatile signal is abolished by the administration of a long-acting synthetic glucocorticoid, the resulting disruption in physiological regulation has the potential to negatively impact many glucocorticoid-dependent bodily systems. Even subtle alterations to the dynamics of the system, during chronic stress or certain disease states, can potentially result in changes in functional output of multiple cells and tissues throughout the body, altering metabolic processes, behavior, affective state, and cognitive function in susceptible individuals. The recent development of a novel chronotherapy, which can deliver both circadian and ultradian patterns, provides great promise for patients on glucocorticoid treatment.
Collapse
Affiliation(s)
- Stafford L Lightman
- Translational Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew T Birnie
- Translational Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | | |
Collapse
|
17
|
Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development 2019; 146:146/19/dev178780. [PMID: 31570369 DOI: 10.1242/dev.178780] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.
Collapse
Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Department of Dermatology, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
18
|
Johnson TA, Chereji RV, Stavreva DA, Morris SA, Hager GL, Clark DJ. Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo. Nucleic Acids Res 2019; 46:203-214. [PMID: 29126175 PMCID: PMC5758879 DOI: 10.1093/nar/gkx1044] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Glucocorticoid hormone plays a major role in metabolism and disease. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. We have addressed the role of chromatin structure in GR binding by mapping nucleosome positions in mouse adenocarcinoma cells. Before hormone treatment, GR-enhancers exist in one of three chromatin states: (i) Nucleosome-depleted enhancers that are DNase I-hypersensitive, associated with the Brg1 chromatin remodeler and flanked by nucleosomes incorporating histone H2A.Z. (ii) Nucleosomal enhancers that are DNase I-hypersensitive, marked by H2A.Z and associated with Brg1. (iii) Nucleosomal enhancers that are inaccessible to DNase I, incorporate little or no H2A.Z and lack Brg1. Hormone-induced GR binding results in nucleosome shifts at all types of GR-enhancer, coinciding with increased recruitment of Brg1. We propose that nucleosome-depleted GR-enhancers are formed and maintained by other transcription factors which recruit Brg1 whereas, at nucleosomal enhancers, GR behaves like a pioneer factor, interacting with nucleosomal sites and recruiting Brg1 to remodel the chromatin.
Collapse
Affiliation(s)
- Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Stephanie A Morris
- Office of Cancer Nanotechnology Research, Center for Strategic Scientific Initiatives, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
19
|
Lodato NJ, Rampersaud A, Waxman DJ. Impact of CAR Agonist Ligand TCPOBOP on Mouse Liver Chromatin Accessibility. Toxicol Sci 2019; 164:115-128. [PMID: 29617930 DOI: 10.1093/toxsci/kfy070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1, 4-bis[2-(3, 5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long noncoding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions. We show that a subset of TCPOBOP-responsive genes cluster within TADs, and that TCPOBOP-induced genes and TCPOBOP-repressed genes are often found in different TADs. Further, using DNase-seq and DNase hypersensitivity site (DHS) analysis, we identified several thousand genomic regions (ΔDHS) where short-term exposure to TCPOBOP induces localized changes (increases or decreases) in mouse liver chromatin accessibility, many of which cluster in TADs together with TCPOBOP-responsive genes. Sites of chromatin opening were highly enriched nearby genes induced by TCPOBOP and chromatin closing was highly enriched nearby genes repressed by TCPOBOP, consistent with TCPOBOP-responsive ΔDHS serving as enhancers and promoters that positively regulate CAR-responsive genes. Gene expression changes lagged behind chromatin opening or closing for a subset of TCPOBOP-responsive ΔDHS. ΔDHS that were specifically responsive to TCPOBOP in male liver were significantly enriched for genomic regions with a basal male bias in chromatin accessibility; however, the male-biased response of hepatocellular carcinoma-related genes to TCPOBOP was not associated with a correspondingly male-biased ΔDHS response. These studies elucidate the genome-wide organization of CAR-responsive genes and of the thousands of associated genomic sites where TCPOBOP exposure induces both rapid and persistent changes in chromatin accessibility.
Collapse
Affiliation(s)
- Nicholas J Lodato
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| |
Collapse
|
20
|
Levendosky RF, Bowman GD. Asymmetry between the two acidic patches dictates the direction of nucleosome sliding by the ISWI chromatin remodeler. eLife 2019; 8:45472. [PMID: 31094676 PMCID: PMC6546392 DOI: 10.7554/elife.45472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/16/2019] [Indexed: 01/15/2023] Open
Abstract
The acidic patch is a functionally important epitope on each face of the nucleosome that affects chromatin remodeling. Although related by 2-fold symmetry of the nucleosome, each acidic patch is uniquely positioned relative to a bound remodeler. An open question is whether remodelers are distinctly responsive to each acidic patch. Previously we reported a method for homogeneously producing asymmetric nucleosomes with distinct H2A/H2B dimers (Levendosky et al., 2016). Here, we use this methodology to show that the Chd1 remodeler from Saccharomyces cerevisiae and ISWI remodelers from human and Drosophila have distinct spatial requirements for the acidic patch. Unlike Chd1, which is equally affected by entry- and exit-side mutations, ISWI remodelers strongly depend on the entry-side acidic patch. Remarkably, asymmetry in the two acidic patches stimulates ISWI to slide mononucleosomes off DNA ends, overriding the remodeler’s preference to shift the histone core toward longer flanking DNA.
Collapse
Affiliation(s)
- Robert F Levendosky
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| |
Collapse
|
21
|
Lorén V, Garcia-Jaraquemada A, Naves JE, Carmona X, Mañosa M, Aransay AM, Lavin JL, Sánchez I, Cabré E, Manyé J, Domènech E. ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach. J Crohns Colitis 2019; 13:351-361. [PMID: 30329026 DOI: 10.1093/ecco-jcc/jjy171] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Steroid-refractoriness is a common and unpredictable phenomenon in ulcerative colitis [UC], but there are no conclusive studies on the molecular functions involved. We aimed to assess the mechanism of action related to steroid failure by integrating transcriptomic data from UC patients, and updated molecular data on UC and glucocorticoids. METHODS MicroRNA [miRNA] and mRNA expression were evaluated by sequencing and microarrays, respectively, from rectal biopsies of patients with moderately-to-severe active UC, obtained before and on the third day of steroid treatment. The differential results were integrated into the mathematical models generated by a systems biology approach. RESULTS This computational approach identified 18 proteins that stand out either by being associated with the mechanism of action or by providing a means to classify the patients according to steroid response. Their biological functions have been linked to inflammation, glucocorticoid-induced transcription and angiogenesis. All the selected proteins except ANP32E [a chaperone which has been linked to the exchange of H2A.z histone and promotes glucocorticoid receptor-induced transcription] had previously been related to UC and/or glucocorticoid-induced biological actions. Western blot and immunofluorescence assays confirmed the implication of this chaperone in steroid failure in patients with active UC. CONCLUSIONS A systems biology approach allowed us to identify a comprehensive mechanism of action of steroid-refractoriness, highlighting the key role of steroid-induced transcription and the potential implication of ANP32E in this phenomenon.
Collapse
Affiliation(s)
- V Lorén
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - A Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - J E Naves
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - X Carmona
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - M Mañosa
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - A M Aransay
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - J L Lavin
- Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - I Sánchez
- Functional Biology and Experimental Therapeutics Laboratory, Functional and Translational Neurogenetics Unit, Department of Neurosciences, Germans Trias i Pujol Research Institute, Badalona, Catalonia, Spain
| | - E Cabré
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - J Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - E Domènech
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| |
Collapse
|
22
|
Pillidge Z, Bray SJ. SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility. EMBO Rep 2019; 20:embr.201846944. [PMID: 30914409 DOI: 10.15252/embr.201846944] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/18/2022] Open
Abstract
Notch signaling plays a key role in many cell fate decisions during development by directing different gene expression programs via the transcription factor CSL, known as Su(H) in Drosophila Which target genes are responsive to Notch signaling is influenced by the chromatin state of enhancers, yet how this is regulated is not fully known. Detecting a specific increase in the histone variant H3.3 in response to Notch signaling, we tested which chromatin remodelers or histone chaperones are required for the changes in enhancer accessibility to Su(H) binding. We show a crucial role for the Brahma SWI/SNF chromatin remodeling complex, including the actin-related BAP55 subunit, in conferring enhancer accessibility and enabling the transcriptional response to Notch activity. The Notch-responsive regions have high levels of nucleosome turnover which depend on the Brahma complex, increase in magnitude with Notch signaling, and primarily involve histone H3.3. Together these results highlight the importance of SWI/SNF-mediated nucleosome turnover in rendering enhancers responsive to Notch.
Collapse
Affiliation(s)
- Zoe Pillidge
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sarah J Bray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| |
Collapse
|
23
|
Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
Collapse
Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
| |
Collapse
|
24
|
Mehta GD, Ball DA, Eriksson PR, Chereji RV, Clark DJ, McNally JG, Karpova TS. Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast. Mol Cell 2018; 72:875-887.e9. [PMID: 30318444 DOI: 10.1016/j.molcel.2018.09.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/08/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
It is unknown how the dynamic binding of transcription factors (TFs) is molecularly linked to chromatin remodeling and transcription. Using single-molecule tracking (SMT), we show that the chromatin remodeler RSC speeds up the search process of the TF Ace1p for its response elements (REs) at the CUP1 promoter. We quantified smFISH mRNA data using a gene bursting model and demonstrated that RSC regulates transcription bursts of CUP1 only by modulating TF occupancy but does not affect initiation and elongation rates. We show by SMT that RSC binds to activated promoters transiently, and based on MNase-seq data, that RSC does not affect the nucleosomal occupancy at CUP1. Therefore, transient binding of Ace1p and rapid bursts of transcription at CUP1 may be dependent on short repetitive cycles of nucleosome mobilization. This type of regulation reduces the transcriptional noise and ensures a homogeneous response of the cell population to heavy metal stress.
Collapse
Affiliation(s)
- Gunjan D Mehta
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Ball
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter R Eriksson
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James G McNally
- Institute for Soft Matter and Functional Materials, Helmholtz Center Berlin, Berlin 12489, Germany
| | - Tatiana S Karpova
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
25
|
Jubb AW, Boyle S, Hume DA, Bickmore WA. Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci. Cell Rep 2018; 21:3022-3031. [PMID: 29241532 PMCID: PMC5745231 DOI: 10.1016/j.celrep.2017.11.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 10/01/2017] [Accepted: 11/15/2017] [Indexed: 12/26/2022] Open
Abstract
Glucocorticoids act by binding to the glucocorticoid receptor (GR), which binds to specific motifs within enhancers of target genes to activate transcription. Previous studies have suggested that GRs can promote interactions between gene promoters and distal elements within target loci. In contrast, we demonstrate here that glucocorticoid addition to mouse bone-marrow-derived macrophages produces very rapid chromatin unfolding detectable by fluorescence in situ hybridization (FISH) at loci associated with GR binding. Rapid chromatin decompaction was generally not dependent on transcription at those loci that are known to be inducible in both mouse and human macrophages and was sustained for up to 5 days following ligand removal. Chromatin decompaction was not dependent upon persistent GR binding, which decayed fully after 24 hr. We suggest that sustained large-scale chromatin reorganization forms an important part of the response to glucocorticoid and might contribute to glucocorticoid sensitivity and resistance. Glucocorticoids can induce rapid and persistent chromatin decompaction Transcription is not essential for chromatin decompaction Large-scale chromatin organization may modulate the glucocorticoid response
Collapse
Affiliation(s)
- Alasdair W Jubb
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK; The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; Department of Medicine, University of Cambridge, Box 93, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; Mater Research-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| |
Collapse
|
26
|
Swinstead EE, Paakinaho V, Hager GL. Chromatin reprogramming in breast cancer. Endocr Relat Cancer 2018; 25:R385-R404. [PMID: 29692347 PMCID: PMC6029727 DOI: 10.1530/erc-18-0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. In this review, we describe what is currently known about the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. Emphasis has been placed on characterizing the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin in breast cancer cells. In addition, we discuss current techniques employed to study enhancer function at a genome-wide level. Further, we have noted recent advances in live cell imaging technology. These single-cell approaches enable the coupling of population-based assays with real-time studies to address many unsolved questions about SRs and chromatin dynamics in breast cancer.
Collapse
Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
- Institute of BiomedicineUniversity of Eastern Finland, Kuopio, Finland
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
| |
Collapse
|
27
|
Lee BH, Stallcup MR. Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5. PLoS One 2018; 13:e0196965. [PMID: 29738565 PMCID: PMC5940187 DOI: 10.1371/journal.pone.0196965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/24/2018] [Indexed: 11/18/2022] Open
Abstract
The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription complexes. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is necessary for glucocorticoid (GC) regulation of one group of GR target genes, is irrelevant for a second group, and inhibits GR binding to a third gene set, thereby blocking their regulation by GC. Gene-specific characteristics that distinguish GR binding regions (GBR) at Hic-5 blocked genes from GBR at other GC-regulated genes are unknown. Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.
Collapse
Affiliation(s)
- Brian H. Lee
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Michael R. Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
28
|
Steube A, Schenk T, Tretyakov A, Saluz HP. High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells. Nat Commun 2017; 8:1303. [PMID: 29101361 PMCID: PMC5670203 DOI: 10.1038/s41467-017-01251-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/31/2017] [Indexed: 01/10/2023] Open
Abstract
Genome-wide mapping of transcription factor binding is generally performed by chemical protein–DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein–DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces an efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein–DNA interactions in their natural environment. Here we show that UV-ChIP-seq, applied for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells, produces sensitive and precise protein–DNA binding profiles, highly enriched with canonical BCL6 DNA sequence motifs. Using this technique, we also found numerous previously undetectable direct BCL6 binding sites, particularly in condensed, inaccessible areas of chromatin. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) can map transcription factor binding to a given genome. Here, Steube and colleagues devise a ChIP-seq technique based on photochemical crosslinking by high-intensity ultraviolet laser irradiation, and describe its utility.
Collapse
Affiliation(s)
- Arndt Steube
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, 07747, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
| | - Tino Schenk
- Friedrich Schiller University, Jena, 07737, Germany. .,Department of Hematology and Medical Oncology, Clinic of Internal Medicine II, Jena University Hospital, Jena, 07747, Germany. .,Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, Jena, 07745, Germany.
| | - Alexander Tretyakov
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany
| | - Hans Peter Saluz
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
| |
Collapse
|
29
|
Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses. Sci Rep 2017; 7:11725. [PMID: 28916762 PMCID: PMC5601431 DOI: 10.1038/s41598-017-12010-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/30/2017] [Indexed: 11/08/2022] Open
Abstract
Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy. Here, we describe a novel application of UV laser-induced (L-) crosslinking and demonstrate that a combination of chemical and L-crosslinking is able to distinguish between direct and indirect DNA-protein interactions in a small number of living cells. The spatial and temporal dynamics of TF bindings to chromatin and their role in gene expression regulation may thus be assessed. The combination of chemical and L-crosslinking offers an exciting and unprecedented tool for biomedical applications.
Collapse
|
30
|
Abstract
Pioneer factors such as FoxA target nucleosomal DNA and initiate cooperative interactions at silent genes during development, cellular reprogramming, and steroid hormone induction. Biophysical studies previously showed that the nuclear mobility of FoxA1 is slower than for many other transcription factors, whereas a new single molecule study (Swinstead et al., 2016, Cell) shows comparable chromatin residence times for FoxA1 and steroid receptors. Despite that steroid receptors engage nucleosome-remodeling complexes, the vast majority of co-bound sites with FoxA are dependent upon FoxA, not vice versa. Taken together, the distinguishing feature of pioneer factors remains nucleosomal access rather than an exceptional residence time in chromatin.
Collapse
Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
| | - Jonathan Lerner
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| |
Collapse
|
31
|
Grbesa I, Hakim O. Genomic effects of glucocorticoids. PROTOPLASMA 2017; 254:1175-1185. [PMID: 28013411 DOI: 10.1007/s00709-016-1063-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Glucocorticoids and their receptor (GR) have been an important area of research because of their pleiotropic physiological functions and extensive use in the clinic. In addition, the association between GR and glucocorticoids, which is highly specific, leads to rapid nuclear translocation where GR associates with chromatin to regulate gene transcription. This simplified model system has been instrumental for studying the complexity of transcription regulation processes occurring at chromatin. In this review we discuss our current understanding of GR action that has been enhanced by recent developments in genome wide measurements of chromatin accessibility, histone marks, chromatin remodeling and 3D chromatin structure in various cell types responding to glucocorticoids.
Collapse
Affiliation(s)
- Ivana Grbesa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel.
| |
Collapse
|
32
|
Lee BH, Stallcup MR. Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes. J Biol Chem 2017; 292:9320-9334. [PMID: 28381557 DOI: 10.1074/jbc.m117.782607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/31/2017] [Indexed: 11/06/2022] Open
Abstract
The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid (GC) regulation of some genes but not others and blocks the regulation of a third gene set by inhibiting GR binding. How Hic-5 exerts these gene-specific effects and specifically how it blocks GR binding to some genes but not others is unclear. Here we show that site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. By depletion of 11 different chromatin remodelers, we found that ATPases chromodomain helicase DNA-binding protein 9 (CHD9) and Brahma homologue (BRM, a product of the SMARCA2 gene) are required for GC-regulated expression of the blocked genes but not for other GC-regulated genes. Furthermore, CHD9 and BRM were required for GR occupancy and chromatin remodeling at GR-binding regions associated with blocked genes but not at GR-binding regions associated with other GC-regulated genes. Hic-5 selectively inhibits GR interaction with CHD9 and BRM, thereby blocking chromatin remodeling and robust GR binding at GR-binding sites associated with blocked genes. Thus, Hic-5 regulates GR binding site selection by a novel mechanism, exploiting gene-specific requirements for chromatin remodeling enzymes to selectively influence DNA occupancy and gene regulation by a transcription factor.
Collapse
Affiliation(s)
- Brian H Lee
- From the Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089-9176
| | - Michael R Stallcup
- From the Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089-9176
| |
Collapse
|
33
|
Abstract
Glucocorticoid hormones (GC) regulate essential physiological functions including energy homeostasis, embryonic and postembryonic development, and the stress response. From the biomedical perspective, GC have garnered a tremendous amount of attention as highly potent anti-inflammatory and immunosuppressive medications indispensable in the clinic. GC signal through the GC receptor (GR), a ligand-dependent transcription factor whose structure, DNA binding, and the molecular partners that it employs to regulate transcription have been under intense investigation for decades. In particular, next-generation sequencing-based approaches have revolutionized the field by introducing a unified platform for a simultaneous genome-wide analysis of cellular activities at the level of RNA production, binding of transcription factors to DNA and RNA, and chromatin landscape and topology. Here we describe fundamental concepts of GC/GR function as established through traditional molecular and in vivo approaches and focus on the novel insights of GC biology that have emerged over the last 10 years from the rapidly expanding arsenal of system-wide genomic methodologies.
Collapse
Affiliation(s)
- Maria A Sacta
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| | - Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021;
| | - Inez Rogatsky
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| |
Collapse
|
34
|
Swinstead EE, Paakinaho V, Presman DM, Hager GL. Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective: Multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factors. Bioessays 2016; 38:1150-1157. [PMID: 27633730 DOI: 10.1002/bies.201600137] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transcription factor (TF) signaling regulates gene transcription and requires a complex network of proteins. This network includes co-activators, co-repressors, multiple TFs, histone-modifying complexes, and the basal transcription machinery. It has been widely appreciated that pioneer factors, such as FoxA1 and GATA1, play an important role in opening closed chromatin regions, thereby allowing binding of a secondary factor. In this review we will focus on a newly proposed model wherein multiple TFs, such as steroid receptors (SRs), can function in a pioneering role. This model, termed dynamic assisted loading, integrates data from widely divergent methodologies, including genome wide ChIP-Seq, digital genomic footprinting, DHS-Seq, live cell protein dynamics, and biochemical studies of ATP-dependent remodeling complexes, to present a real time view of TF chromatin interactions. Under this view, many TFs can act as initiating factors for chromatin landscape programming. Furthermore, enhancer and promoter states are more accurately described as energy-dependent, non-equilibrium steady states.
Collapse
Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA.
| |
Collapse
|
35
|
Smirnova OV. Competitive Agonists and Antagonists of Steroid Nuclear Receptors: Evolution of the Concept or Its Reversal. BIOCHEMISTRY (MOSCOW) 2016; 80:1227-34. [PMID: 26567566 DOI: 10.1134/s000629791510003x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mechanisms displaying pure and mixed steroid agonist/antagonist activity as well as principles underlying in vivo action of selective steroid receptor modulators dependent on tissue or cell type including interaction with various types of nuclear receptors are analyzed in this work. Mechanisms of in vitro action for mixed agonist/antagonist steroids are discussed depending on: specific features of their interaction with receptor hormone-binding pocket; steroid-dependent allosteric modulation of interaction between hormone-receptor complex and hormone response DNA elements; features of interacting hormone-receptor complex with protein transcriptional coregulators; level and tissue-specific composition of transcriptional coregulators. A novel understanding regarding context-selective modulators replacing the concept of steroid agonists and antagonists is discussed.
Collapse
Affiliation(s)
- O V Smirnova
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia.
| |
Collapse
|
36
|
Mazina MY, Vorobyeva NE. The role of ATP-dependent chromatin remodeling complexes in regulation of genetic processes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416050082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
37
|
Swinstead EE, Miranda TB, Paakinaho V, Baek S, Goldstein I, Hawkins M, Karpova TS, Ball D, Mazza D, Lavis LD, Grimm JB, Morisaki T, Grøntved L, Presman DM, Hager GL. Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions. Cell 2016; 165:593-605. [PMID: 27062924 DOI: 10.1016/j.cell.2016.02.067] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/12/2016] [Accepted: 02/25/2016] [Indexed: 02/08/2023]
Abstract
The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression. FoxA1 has been implicated in establishing ER-binding patterns though its unique ability to serve as a pioneer factor. However, the molecular interplay between ER, GR, and FoxA1 requires further investigation. Here we show that ER and GR both have the ability to alter the genomic distribution of the FoxA1 pioneer factor. Single-molecule tracking experiments in live cells reveal a highly dynamic interaction of FoxA1 with chromatin in vivo. Furthermore, the FoxA1 factor is not associated with detectable footprints at its binding sites throughout the genome. These findings support a model wherein interactions between transcription factors and pioneer factors are highly dynamic. Moreover, at a subset of genomic sites, the role of pioneer can be reversed, with the steroid receptors serving to enhance binding of FoxA1.
Collapse
Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Tina B Miranda
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Mary Hawkins
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale e Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tatsuya Morisaki
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, NCI, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
38
|
McKnight JN, Tsukiyama T, Bowman GD. Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler. Genome Res 2016; 26:693-704. [PMID: 26993344 PMCID: PMC4864466 DOI: 10.1101/gr.199919.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 03/14/2016] [Indexed: 01/15/2023]
Abstract
ATP-dependent chromatin remodelers regulate chromatin dynamics by modifying nucleosome positions and occupancy. DNA-dependent processes such as replication and transcription rely on chromatin to faithfully regulate DNA accessibility, yet how chromatin remodelers achieve well-defined nucleosome positioning in vivo is poorly understood. Here, we report a simple method for site-specifically altering nucleosome positions in live cells. By fusing the Chd1 remodeler to the DNA binding domain of the Saccharomyces cerevisiae Ume6 repressor, we have engineered a fusion remodeler that selectively positions nucleosomes on top of adjacent Ume6 binding motifs in a highly predictable and reproducible manner. Positioning of nucleosomes by the fusion remodeler recapitulates closed chromatin structure at Ume6-sensitive genes analogous to the endogenous Isw2 remodeler. Strikingly, highly precise positioning of single founder nucleosomes by either chimeric Chd1-Ume6 or endogenous Isw2 shifts phased chromatin arrays in cooperation with endogenous chromatin remodelers. Our results demonstrate feasibility of engineering precise nucleosome rearrangements through sequence-targeted chromatin remodeling and provide insight into targeted action and cooperation of endogenous chromatin remodelers in vivo.
Collapse
Affiliation(s)
- Jeffrey N McKnight
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| |
Collapse
|
39
|
Runge JS, Raab JR, Magnuson T. Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes: SNF-ing Out Crosstalk. Curr Top Dev Biol 2016; 117:1-13. [PMID: 26969969 DOI: 10.1016/bs.ctdb.2015.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cells utilize precise mechanisms to access genomic DNA with spatiotemporal accuracy. ATP-dependent chromatin-remodeling enzymes (also known simply as "remodelers") comprise a specialized class of enzymes that is intimately involved in genomic organization and accessibility. Remodelers selectively position nucleosomes to either alleviate chromatin compaction or achieve genomic condensation locally, based on a multitude of cellular signals. By dictating nucleosome position, remodelers control local euchromatic and heterochromatic states. These activities govern the accessibility of regulatory regions like promoters and enhancers to transcription factors, RNA polymerases, and coactivators or -repressors. As studies unravel the complexities of epigenetic topography, evidence points to a chromatin-based interactome where regulators interact competitively, cooperatively, and/or codependently through physical and functional means. These types of interactions, or crosstalk, between remodelers raise important questions for tissue development. Here, we briefly review the evidence for remodeler interactions and argue for additional studies examining crosstalk.
Collapse
Affiliation(s)
- John S Runge
- Curriculum for Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jesse R Raab
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
| |
Collapse
|
40
|
Wiley JW, Higgins GA, Athey BD. Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis. Neurogastroenterol Motil 2016; 28:12-25. [PMID: 26690871 PMCID: PMC4688904 DOI: 10.1111/nmo.12706] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/20/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND Chronic psychological stress is associated with enhanced abdominal pain and altered intestinal barrier function that may result from a perturbation in the hypothalamic-pituitary-adrenal (HPA) axis. The glucocorticoid receptor (GR) exploits diverse mechanisms to activate or suppress congeneric gene expression, with regulatory variation associated with stress-related disorders in psychiatry and gastroenterology. PURPOSE During acute and chronic stress, corticotropin-releasing hormone drives secretion of adrenocorticotropic hormone from the pituitary, ultimately leading to the release of cortisol (human) and corticosterone (rodent) from the adrenal glands. Cortisol binds with the GR in the cytosol, translocates to the nucleus, and activates the NR3C1 (nuclear receptor subfamily 3, group C, member 1 [GR]) gene. This review focuses on the rapidly developing observations that cortisol is responsible for driving circadian and ultradian bursts of transcriptional activity in the CLOCK (clock circadian regulator) and PER (period circadian clock 1) gene families, and this rhythm is disrupted in major depressive disorder, bipolar disorder, and stress-related gastrointestinal and immune disorders. Glucocorticoid receptor regulates different sets of transcripts in a tissue-specific manner, through pulsatile waves of gene expression that includes occupancy of glucocorticoid response elements located within constitutively open spatial domains in chromatin. Emerging evidence supports a potentially pivotal role for epigenetic regulation of how GR interacts with other chromatin regulators to control the expression of its target genes. Dysregulation of the central and peripheral GR regulome has potentially significant consequences for stress-related disorders affecting the brain-gut axis.
Collapse
Affiliation(s)
- John W. Wiley
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Gerald A. Higgins
- Department of Pharmacogenomic Science, Assurex Health, Inc., 6030 South Mason Montgomery Road, Mason, OH 45040, USA,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Brian D. Athey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| |
Collapse
|
41
|
Abstract
Mammals have at least 210 histologically diverse cell types (Alberts, Molecular biology of the cell. Garland Science, New York, 2008) and the number would be even higher if functional differences are taken into account. The genome in each of these cell types is differentially programmed to express the specific set of genes needed to fulfill the phenotypical requirements of the cell. Furthermore, in each of these cell types, the gene program can be differentially modulated by exposure to external signals such as hormones or nutrients. The basis for the distinct gene programs relies on cell type-selective activation of transcriptional enhancers, which in turn are particularly sensitive to modulation. Until recently we had only fragmented insight into the regulation of a few of these enhancers; however, the recent advances in high-throughput sequencing technologies have enabled the development of a large number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level.
Collapse
Affiliation(s)
- Alexander Rauch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark.
| |
Collapse
|
42
|
De Angelis RW, Maluf NK, Yang Q, Lambert JR, Bain DL. Glucocorticoid Receptor-DNA Dissociation Kinetics Measured in Vitro Reveal Exchange on the Second Time Scale. Biochemistry 2015; 54:5306-14. [PMID: 26267475 DOI: 10.1021/acs.biochem.5b00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The glucocorticoid receptor (GR) is a member of the steroid receptor family of ligand-activated transcription factors. Recent live cell imaging studies have revealed that interactions of GR with chromatin are highly dynamic, with average receptor residence times of only seconds. These findings were surprising because early kinetic studies found that GR-DNA interactions in vitro were much slower, having calculated residence times of minutes to hours. However, these latter analyses were conducted at a time when it was possible to work with only either partially purified holoreceptor or its purified but isolated DNA binding domain. Noting these limitations, we reexamined GR-DNA dissociation kinetics using a highly purified holoreceptor shown to be amenable to rigorous study. We first observe that GR-DNA interactions in vitro are not slow as previously thought but converge with in vivo behavior, having residence times of only seconds to tens of seconds. This rapid exchange is seen at six individual response elements and the multisite MMTV promoter used in live cell imaging. Second, GR dissociation rates are identical for all response elements. Thus, previously observed differences in receptor affinity toward these sequences are not due to differences in off rate but in on rate. Finally, dissociation kinetics are biphasic in character. A minimal kinetic model consistent with the data is that in which DNA-bound GR interconverts between states on a second time scale, with dissociation occurring via a multistep process. We speculate that receptor interconversion in this time frame can be recognized by the coregulatory proteins that interact with GR, leading to unique transcriptional responses.
Collapse
Affiliation(s)
- Rolando W De Angelis
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Nasib K Maluf
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Qin Yang
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - James R Lambert
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - David L Bain
- Department of Pharmaceutical Sciences and ‡Department of Pathology, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| |
Collapse
|
43
|
Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. Dynamic regulation of transcription factors by nucleosome remodeling. eLife 2015; 4. [PMID: 26047462 PMCID: PMC4456607 DOI: 10.7554/elife.06249] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/11/2015] [Indexed: 12/27/2022] Open
Abstract
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes. DOI:http://dx.doi.org/10.7554/eLife.06249.001 Cells contain thousands of genes that are encoded by molecules of DNA. In yeast and other eukaryotic organisms, this DNA is wrapped around proteins called histones to make structures called nucleosomes. This compacts the DNA and allows it to fit inside the tiny nucleus within the cell. The positioning of the nucleosomes influences how tightly packed the DNA is, which in turn influences the activity of genes. Less active genes tend to be found within regions of DNA that are tightly packed, while more active genes are found in less tightly packed regions. To activate a gene, proteins called transcription factors bind to a section of DNA within the gene called the promoter. Enzymes known as ‘chromatin remodelers’ can alter the locations of nucleosomes on DNA to allow the transcription factors access to the promoters of particular genes. In yeast, the SWI/SNF family of chromatin remodelers can disassemble nucleosomes to promote gene activity, while the ISW1 family organises nucleosomes into closely spaced groups to repress gene activity. However, it is not clear if, or how, chromatin remodelers can influence transcription factors that are already bound to DNA. Here, Li et al. studied the interactions between a transcription factor and the chromatin remodelers in yeast. The experiment used a piece of DNA that contained a bound transcription factor and a single nucleosome. Li et al. used a technique called ‘single molecule DNA unzipping’, which enabled them to precisely locate the position of the nucleosome and transcription factor before and after the nucleosome was remodeled. The experiments found that a chromatin remodeler called ISW1a moved the nucleosome away from the transcription factor, while a SWI/SNF chromatin remodeler moved the nucleosome towards it. Significantly, Li et al. also found that a transcription factor is a major barrier to ISW1a's remodeling activity, suggesting that ISW1a may use transcription factors as reference points to position nucleosomes. In contrast, SWI/SNF was able to slide a nucleosome past the transcription factor, which led to the transcription factor falling off the DNA. Therefore, SWI/SNF is able to move transcription factors out of the way to deactivate genes. Li et al. propose a new model for how chromatin remodelers can move nucleosomes and regulate transcription factors to alter gene activity. A future challenge will be to observe these types of activities in living cells. DOI:http://dx.doi.org/10.7554/eLife.06249.002
Collapse
Affiliation(s)
- Ming Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Arjan Hada
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Payel Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Lola Olufemi
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michael A Hall
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Benjamin Y Smith
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Scott Forth
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Jeffrey N McKnight
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ashok Patel
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Blaine Bartholomew
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| |
Collapse
|
44
|
Helzer KT, Hooper C, Miyamoto S, Alarid ET. Ubiquitylation of nuclear receptors: new linkages and therapeutic implications. J Mol Endocrinol 2015; 54:R151-67. [PMID: 25943391 PMCID: PMC4457637 DOI: 10.1530/jme-14-0308] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 12/25/2022]
Abstract
The nuclear receptor (NR) superfamily is a group of transcriptional regulators that control multiple aspects of both physiology and pathology and are broadly recognized as viable therapeutic targets. While receptor-modulating drugs have been successful in many cases, the discovery of new drug targets is still an active area of research, because resistance to NR-targeting therapies remains a significant clinical challenge. Many successful targeted therapies have harnessed the control of receptor activity by targeting events within the NR signaling pathway. In this review, we explore the role of NR ubiquitylation and discuss how the expanding roles of ubiquitin could be leveraged to identify additional entry points to control receptor function for future therapeutic development.
Collapse
Affiliation(s)
- Kyle T Helzer
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Christopher Hooper
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Shigeki Miyamoto
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Elaine T Alarid
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| |
Collapse
|
45
|
Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
| |
Collapse
|
46
|
Sung MH, Guertin MJ, Baek S, Hager GL. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 2014; 56:275-285. [PMID: 25242143 DOI: 10.1016/j.molcel.2014.08.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/05/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022]
Abstract
Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a timescale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor-binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach.
Collapse
Affiliation(s)
- Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Michael J Guertin
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
47
|
Connaghan KD, Yang Q, Miura MT, Moody AD, Bain DL. Homologous steroid receptors assemble at identical promoter architectures with unique energetics of cooperativity. Proteins 2014; 82:2078-87. [PMID: 24648119 DOI: 10.1002/prot.24563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/05/2014] [Accepted: 03/14/2014] [Indexed: 01/27/2023]
Abstract
Steroid receptors comprise a homologous family of ligand-activated transcription factors. The receptors bind largely identical response elements in vitro, yet regulate distinct gene networks in vivo. This paradox raises the issue of how transcriptional specificity is achieved, particularly if multiple receptor populations are competing for identical sites. Noting that receptor-DNA energetics are a primary force in driving transcriptional activity, differences in interaction energetics among the receptors might underlie receptor-specific transcriptional control. Thermodynamic dissections support this premise-upon assembling at an identical promoter architecture, individual receptors exhibit vast differences in cooperative and self-association energetics. More intriguingly, these parameters distribute in a way that mirrors the evolutionary divergence of the steroid receptor family. For example, the closely related progesterone and glucocorticoid receptors (PR and GR) display little or no self-association but strong intersite cooperativity, whereas the more distantly related estrogen receptor (ER-α) shows inverse behavior. These findings suggest that receptors view genomic promoter architectures as a collection of affinity landscapes; receptors select from this landscape via their unique interaction energetics. To test this idea, we analyzed the cooperative binding energetics of the above three receptors using an array of promoters. We find that cooperativity is not only receptor-specific but also highly promoter-specific. Thus PR shows maximal cooperativity at promoters with closely spaced and in phase binding sites. GR cooperativity is maintained over greater distances, is larger energetically, and shows markedly different phase dependency. Finally, ER-α appears incapable of cooperativity regardless of promoter architecture, consistent with its more distant phylogeny.
Collapse
Affiliation(s)
- Keith D Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045
| | | | | | | | | |
Collapse
|
48
|
Menet JS, Pescatore S, Rosbash M. CLOCK:BMAL1 is a pioneer-like transcription factor. Genes Dev 2014; 28:8-13. [PMID: 24395244 PMCID: PMC3894415 DOI: 10.1101/gad.228536.113] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/27/2013] [Indexed: 11/28/2022]
Abstract
The mammalian circadian clock relies on the master genes CLOCK and BMAL1 to drive rhythmic gene expression and regulate biological functions under circadian control. Here we show that rhythmic CLOCK:BMAL1 DNA binding promotes rhythmic chromatin opening. Mechanisms include CLOCK:BMAL1 binding to nucleosomes and rhythmic chromatin modification; e.g., incorporation of the histone variant H2A.Z. This rhythmic chromatin remodeling mediates the rhythmic binding of other transcription factors adjacent to CLOCK:BMAL1, suggesting that the activity of these other transcription factors contributes to the genome-wide CLOCK:BMAL1 heterogeneous transcriptional output. These data therefore indicate that the clock regulation of transcription relies on the rhythmic regulation of chromatin accessibility and suggest that the concept of pioneer function extends to acute gene regulation.
Collapse
Affiliation(s)
| | - Stefan Pescatore
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| |
Collapse
|
49
|
Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat Rev Genet 2013; 15:69-81. [PMID: 24342920 DOI: 10.1038/nrg3623] [Citation(s) in RCA: 333] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The interaction of regulatory proteins with the complex nucleoprotein structures that are found in mammalian cells involves chromatin reorganization at multiple levels. Mechanisms that support these transitions are complex on many timescales, which range from milliseconds to minutes or hours. In this Review, we discuss emerging concepts regarding the function of regulatory elements in living cells. We also explore the involvement of these dynamic and stochastic processes in the evolution of fluctuating transcriptional activity states that are now commonly reported in eukaryotic systems.
Collapse
|
50
|
Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions. Nat Struct Mol Biol 2013; 21:73-81. [PMID: 24317492 PMCID: PMC3947387 DOI: 10.1038/nsmb.2718] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 10/17/2013] [Indexed: 12/24/2022]
Abstract
ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.
Collapse
Affiliation(s)
- Stephanie A Morris
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|