1
|
Ramírez-Cuéllar J, Ferrari R, Sanz RT, Valverde-Santiago M, García-García J, Nacht AS, Castillo D, Le Dily F, Neguembor MV, Malatesta M, Bonnin S, Marti-Renom MA, Beato M, Vicent GP. LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells. EMBO J 2024; 43:1770-1798. [PMID: 38565950 PMCID: PMC11066098 DOI: 10.1038/s44318-024-00080-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.
Collapse
Affiliation(s)
- Julieta Ramírez-Cuéllar
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosario T Sanz
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - Marta Valverde-Santiago
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - Judith García-García
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Maria Victoria Neguembor
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sarah Bonnin
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Marc A Marti-Renom
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
- ICREA, Barcelona, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain.
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain.
| |
Collapse
|
2
|
Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
Collapse
Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
| |
Collapse
|
3
|
Miao T, Symonds A, Hickman OJ, Wu D, Wang P, Lemoine N, Wang Y, Linardopoulos S, Halldén G. Inhibition of Bromodomain Proteins Enhances Oncolytic HAdVC5 Replication and Efficacy in Pancreatic Ductal Adenocarcinoma (PDAC) Models. Int J Mol Sci 2024; 25:1265. [PMID: 38279262 PMCID: PMC10816486 DOI: 10.3390/ijms25021265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most aggressive type of pancreatic cancer, which rapidly develops resistance to the current standard of care. Several oncolytic Human AdenoViruses (HAdVs) have been reported to re-sensitize drug-resistant cancer cells and in combination with chemotherapeutics attenuate solid tumour growth. Obstacles preventing greater clinical success are rapid hepatic elimination and limited viral replication and spread within the tumour microenvironment. We hypothesised that higher intratumoural levels of the virus could be achieved by altering cellular epigenetic regulation. Here we report on the screening of an enriched epigenetics small molecule library and validation of six compounds that increased viral gene expression and replication. The greatest effects were observed with three epigenetic inhibitors targeting bromodomain (BRD)-containing proteins. Specifically, BRD4 inhibitors enhanced the efficacy of Ad5 wild type, Ad∆∆, and Ad-3∆-A20T in 3-dimensional co-culture models of PDAC and in vivo xenografts. RNAseq analysis demonstrated that the inhibitors increased viral E1A expression, altered expression of cell cycle regulators and inflammatory factors, and attenuated expression levels of tumour cell oncogenes such as c-Myc and Myb. The data suggest that the tumour-selective Ad∆∆ and Ad-3∆-A20T combined with epigenetic inhibitors is a novel strategy for the treatment of PDAC by eliminating both cancer and associated stromal cells to pave the way for immune cell access even after systemic delivery of the virus.
Collapse
Affiliation(s)
- Tizong Miao
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (T.M.); (N.L.); (Y.W.)
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (A.S.); (P.W.)
| | - Alistair Symonds
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (A.S.); (P.W.)
| | - Oliver J. Hickman
- Cancer Drug Target Discovery Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; (O.J.H.); (S.L.)
| | - Dongsheng Wu
- Bioimaging Centre, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK;
| | - Ping Wang
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (A.S.); (P.W.)
| | - Nick Lemoine
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (T.M.); (N.L.); (Y.W.)
| | - Yaohe Wang
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (T.M.); (N.L.); (Y.W.)
| | - Spiros Linardopoulos
- Cancer Drug Target Discovery Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; (O.J.H.); (S.L.)
| | - Gunnel Halldén
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (T.M.); (N.L.); (Y.W.)
| |
Collapse
|
4
|
Di Vona C, Barba L, Ferrari R, de la Luna S. Loss of the DYRK1A Protein Kinase Results in the Reduction in Ribosomal Protein Gene Expression, Ribosome Mass and Reduced Translation. Biomolecules 2023; 14:31. [PMID: 38254631 PMCID: PMC10813206 DOI: 10.3390/biom14010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Ribosomal proteins (RPs) are evolutionary conserved proteins that are essential for protein translation. RP expression must be tightly regulated to ensure the appropriate assembly of ribosomes and to respond to the growth demands of cells. The elements regulating the transcription of RP genes (RPGs) have been characterized in yeast and Drosophila, yet how cells regulate the production of RPs in mammals is less well understood. Here, we show that a subset of RPG promoters is characterized by the presence of the palindromic TCTCGCGAGA motif and marked by the recruitment of the protein kinase DYRK1A. The presence of DYRK1A at these promoters is associated with the enhanced binding of the TATA-binding protein, TBP, and it is negatively correlated with the binding of the GABP transcription factor, establishing at least two clusters of RPGs that could be coordinately regulated. However, DYRK1A silencing leads to a global reduction in RPGs mRNAs, pointing at DYRK1A activities beyond those dependent on its chromatin association. Significantly, cells in which DYRK1A is depleted have reduced RP levels, fewer ribosomes, reduced global protein synthesis and a smaller size. We therefore propose a novel role for DYRK1A in coordinating the expression of genes encoding RPs, thereby controlling cell growth in mammals.
Collapse
Affiliation(s)
- Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Laura Barba
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 23/A, 43124 Parma, Italy;
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
5
|
Wrede D, Bordak M, Abraham Y, Mehedi M. Pulmonary Pathogen-Induced Epigenetic Modifications. EPIGENOMES 2023; 7:13. [PMID: 37489401 PMCID: PMC10366755 DOI: 10.3390/epigenomes7030013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
Epigenetics generally involves genetic control by factors other than our own DNA sequence. Recent research has focused on delineating the mechanisms of two major epigenetic phenomena: DNA methylation and histone modification. As epigenetics involves many cellular processes, it is no surprise that it can also influence disease-associated gene expression. A direct link between respiratory infections, host cell epigenetic regulations, and chronic lung diseases is still unknown. Recent studies have revealed bacterium- or virus-induced epigenetic changes in the host cells. In this review, we focused on respiratory pathogens (viruses, bacteria, and fungi) induced epigenetic modulations (DNA methylation and histone modification) that may contribute to lung disease pathophysiology by promoting host defense or allowing pathogen persistence.
Collapse
Affiliation(s)
| | | | | | - Masfique Mehedi
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (D.W.); (M.B.); (Y.A.)
| |
Collapse
|
6
|
Vezzoli M, de Llobet Cucalon LI, Di Vona C, Morselli M, Montanini B, de la Luna S, Teichmann M, Dieci G, Ferrari R. TFIIIC as a Potential Epigenetic Modulator of Histone Acetylation in Human Stem Cells. Int J Mol Sci 2023; 24:ijms24043624. [PMID: 36835038 PMCID: PMC9961906 DOI: 10.3390/ijms24043624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Regulation of histone acetylation dictates patterns of gene expression and hence cell identity. Due to their clinical relevance in cancer biology, understanding how human embryonic stem cells (hESCs) regulate their genomic patterns of histone acetylation is critical, but it remains largely to be investigated. Here, we provide evidence that acetylation of histone H3 lysine-18 (H3K18ac) and lysine-27 (H3K27ac) is only partially established by p300 in stem cells, while it represents the main histone acetyltransferase (HAT) for these marks in somatic cells. Our analysis reveals that whereas p300 marginally associated with H3K18ac and H3K27ac in hESCs, it largely overlapped with these histone marks upon differentiation. Interestingly, we show that H3K18ac is found at "stemness" genes enriched in RNA polymerase III transcription factor C (TFIIIC) in hESCs, whilst lacking p300. Moreover, TFIIIC was also found in the vicinity of genes involved in neuronal biology, although devoid of H3K18ac. Our data suggest a more complex pattern of HATs responsible for histone acetylations in hESCs than previously considered, suggesting a putative role for H3K18ac and TFIIIC in regulating "stemness" genes as well as genes associated with neuronal differentiation of hESCs. The results break ground for possible new paradigms for genome acetylation in hESCs that could lead to new avenues for therapeutic intervention in cancer and developmental diseases.
Collapse
Affiliation(s)
- Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | | | - Chiara Di Vona
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Susana de la Luna
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Martin Teichmann
- Université de Bordeaux INSERM U1312 (Bordeaux Institute of Oncology) 146, rue Léo Saignat, 33076 Bordeaux, France
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Correspondence:
| |
Collapse
|
7
|
Rodríguez MDCR, Rodríguez IG, Nattress C, Qureshi A, Halldén G. HDAC Inhibitors Enhance Efficacy of the Oncolytic Adenoviruses Ad∆∆ and Ad-3∆-A20T in Pancreatic and Triple-Negative Breast Cancer Models. Viruses 2022; 14:1006. [PMID: 35632748 PMCID: PMC9143155 DOI: 10.3390/v14051006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
The prognosis for triple-negative breast cancer (TNBC) and pancreatic ductal adenocarcinoma (PDAC) is dismal. TNBC and PDAC are highly aggressive cancers with few treatment options and a potential for rapid resistance to standard-of-care chemotherapeutics. Oncolytic adenoviruses (OAds) represent a promising tumour-selective strategy that can overcome treatment resistance and eliminate cancer cells by lysis and host immune activation. We demonstrate that histone deacetylase inhibitors (HDACi) potently enhanced the cancer-cell killing of our OAds, Ad∆∆ and Ad-3∆-A20T in TNBC and PDAC preclinical models. In the TNBC cell lines MDA-MB-436, SUM159 and CAL51, cell killing, viral uptake and replication were increased when treated with sublethal doses of the Class-I-selective HDACis Scriptaid, Romidepsin and MS-275. The pan-HDACi, TSA efficiently improved OAd efficacy, both in vitro and in SUM159 xenograft models in vivo. Cell killing and Ad∆∆ replication was also significantly increased in five PDAC cell lines when pre-treated with TSA. Efficacy was dependent on treatment time and dose, and on the specific genetic alterations in each cell line. Expression of the cancer specific αvß6-integrin supported higher viral uptake of the integrin-retargeted Ad-3∆-A20T in combination with Scriptaid. In conclusion, we demonstrate that inhibition of specific HDACs is a potential means to enhance OAd activity, supporting clinical translation.
Collapse
Affiliation(s)
| | - Inés García Rodríguez
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Callum Nattress
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, London WC1E 6DD, UK;
| | - Ahad Qureshi
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (M.D.C.R.R.); (A.Q.)
| | - Gunnel Halldén
- Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (M.D.C.R.R.); (A.Q.)
| |
Collapse
|
8
|
Intranuclear HSV-1 DNA ejection induces major mechanical transformations suggesting mechanoprotection of nucleus integrity. Proc Natl Acad Sci U S A 2022; 119:2114121119. [PMID: 35197285 PMCID: PMC8892323 DOI: 10.1073/pnas.2114121119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
Maintaining nuclear integrity is essential to cell survival when exposed to mechanical stress. Herpesviruses, like most DNA and some RNA viruses, put strain on the nuclear envelope as hundreds of viral DNA genomes replicate and viral capsids assemble. It remained unknown, however, how nuclear mechanics is affected at the initial stage of herpesvirus infection-immediately after viral genomes are ejected into the nuclear space-and how nucleus integrity is maintained despite an increased strain on the nuclear envelope. With an atomic force microscopy force volume mapping approach on cell-free reconstituted nuclei with docked herpes simplex type 1 (HSV-1) capsids, we explored the mechanical response of the nuclear lamina and the chromatin to intranuclear HSV-1 DNA ejection into an intact nucleus. We discovered that chromatin stiffness, measured as Young's modulus, is increased by ∼14 times, while nuclear lamina underwent softening. Those transformations could be associated with a mechanism of mechanoprotection of nucleus integrity facilitating HSV-1 viral genome replication. Indeed, stiffening of chromatin, which is tethered to the lamina meshwork, helps to maintain nuclear morphology. At the same time, increased lamina elasticity, reflected by nucleus softening, acts as a "shock absorber," dissipating the internal mechanical stress on the nuclear membrane (located on top of the lamina wall) and preventing its rupture.
Collapse
|
9
|
Zaurin R, Ferrari R, Nacht AS, Carbonell J, Le Dily F, Font-Mateu J, de Llobet Cucalon LI, Vidal E, Lioutas A, Beato M, Vicent GP. A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations. Nucleic Acids Res 2021; 49:12716-12731. [PMID: 34850111 PMCID: PMC8682742 DOI: 10.1093/nar/gkab1125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels found around the menopause, progesterone receptor (PR) binds only to 2800 genomic sites, which are accessible to ATAC cleavage prior to hormone exposure. These highly accessible sites (HAs) are surrounded by well-organized nucleosomes and exhibit breast enhancer features, including estrogen receptor alpha (ERα), higher FOXA1 and BRD4 (bromodomain containing 4) occupancy. Although HAs are enriched in RAD21 and CTCF, PR binding is the driving force for the most robust interactions with hormone-regulated genes. HAs show higher frequency of 3D contacts among themselves than with other PR binding sites, indicating colocalization in similar compartments. Gene regulation via HAs is independent of classical coregulators and ATP-activated remodelers, relying mainly on MAP kinase activation that enables PR nuclear engagement. HAs are also preferentially occupied by PR and ERα in breast cancer xenografts derived from MCF-7 cells as well as from patients, indicating their potential usefulness as targets for therapeutic intervention.
Collapse
Affiliation(s)
- Roser Zaurin
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Ana Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jose Carbonell
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jofre Font-Mateu
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, 08003, Spain
| |
Collapse
|
10
|
Abstract
Viral infection is intrinsically linked to the capacity of the virus to generate progeny. Many DNA and some RNA viruses need to access the nuclear machinery and therefore transverse the nuclear envelope barrier through the nuclear pore complex. Viral genomes then become chromatinized either in their episomal form or upon integration into the host genome. Interactions with host DNA, transcription factors or nuclear bodies mediate their replication. Often interfering with nuclear functions, viruses use nuclear architecture to ensure persistent infections. Discovering these multiple modes of replication and persistence served in unraveling many important nuclear processes, such as nuclear trafficking, transcription, and splicing. Here, by using examples of DNA and RNA viral families, we portray the nucleus with the virus inside.
Collapse
Affiliation(s)
- Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ines J de Castro
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| |
Collapse
|
11
|
INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins. Cell Rep 2021; 32:108106. [PMID: 32905765 PMCID: PMC7540730 DOI: 10.1016/j.celrep.2020.108106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/26/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast· INO80C recruitment requires origin sequences but does not require ORC· suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs· INO80C co-localizes at origins with Mot1 and NC2 transcription factors· and genetic studies suggest that they function together to promote genome stability. Interestingly· nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences· and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription· maintaining genomic stability. The INO80C chromatin remodeler is known to regulate transcription and genomic stability. Topal et al. find that INO80C functions with Mot1 repressor to prevent pervasive transcription at replication origins in yeast and mESCs. Increased ncRNAs lead to new DNA double-strand breaks at origins, linking transcriptional regulation to genomic stability.
Collapse
|
12
|
Hsu E, Zemke NR, Berk AJ. Promoter-specific changes in initiation, elongation, and homeostasis of histone H3 acetylation during CBP/p300 inhibition. eLife 2021; 10:63512. [PMID: 33704060 PMCID: PMC8009678 DOI: 10.7554/elife.63512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Regulation of RNA polymerase II (Pol2) elongation in the promoter-proximal region is an important and ubiquitous control point for gene expression in metazoans. We report that transcription of the adenovirus 5 E4 region is regulated during the release of paused Pol2 into productive elongation by recruitment of the super-elongation complex, dependent on promoter H3K18/27 acetylation by CBP/p300. We also establish that this is a general transcriptional regulatory mechanism that applies to ~7% of expressed protein-coding genes in primary human airway epithelial cells. We observed that a homeostatic mechanism maintains promoter, but not enhancer, H3K18/27ac in response to extensive inhibition of CBP/p300 acetyl transferase activity by the highly specific small molecule inhibitor A-485. Further, our results suggest a function for BRD4 association at enhancers in regulating paused Pol2 release at nearby promoters. Taken together, our results uncover the processes regulating transcriptional elongation by promoter region histone H3 acetylation and homeostatic maintenance of promoter, but not enhancer, H3K18/27ac in response to inhibition of CBP/p300 acetyl transferase activity.
Collapse
Affiliation(s)
- Emily Hsu
- Molecular Biology Institute, UCLA, Los Angeles, United States
| | - Nathan R Zemke
- Molecular Biology Institute, UCLA, Los Angeles, United States
| | - Arnold J Berk
- Molecular Biology Institute, UCLA, Los Angeles, United States.,Department of Microbiology, UCLA, Los Angeles, United States
| |
Collapse
|
13
|
Abstract
Viral genomes encode transcriptional regulators that alter the expression of viral and host genes. Despite an emerging role in human diseases, a thorough annotation of human viral transcriptional regulators (vTRs) is currently lacking, limiting our understanding of their molecular features and functions. Here, we provide a comprehensive catalog of 419 vTRs belonging to 20 different virus families. Using this catalog, we characterize shared and unique cellular genes, proteins, and pathways targeted by particular vTRs and discuss the role of vTRs in human disease pathogenesis. Our study provides a unique and valuable resource for the fields of virology, genomics, and human disease genetics.
Collapse
|
14
|
Regulation of gene expression by protein lysine acetylation in Salmonella. J Microbiol 2020; 58:979-987. [PMID: 33201432 DOI: 10.1007/s12275-020-0483-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNA-binding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.
Collapse
|
15
|
Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
Collapse
Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
16
|
Lynch KL, Gooding LR, Garnett-Benson C, Ornelles DA, Avgousti DC. Epigenetics and the dynamics of chromatin during adenovirus infections. FEBS Lett 2019; 593:3551-3570. [PMID: 31769503 DOI: 10.1002/1873-3468.13697] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/26/2022]
Abstract
The DNA genome of eukaryotic cells is compacted by histone proteins within the nucleus to form chromatin. Nuclear-replicating viruses such as adenovirus have evolved mechanisms of chromatin manipulation to promote infection and subvert host defenses. Epigenetic factors may also regulate persistent adenovirus infection and reactivation in lymphoid tissues. In this review, we discuss the viral proteins E1A and protein VII that interact with and alter host chromatin, as well as E4orf3, which separates host chromatin from sites of viral replication. We also highlight recent advances in chromatin technologies that offer new insights into virus-directed chromatin manipulation. Beyond the role of chromatin in the viral replication cycle, we discuss the nature of persistent viral genomes in lymphoid tissue and cell lines, and the potential contribution of epigenetic signals in maintaining adenovirus in a quiescent state. By understanding the mechanisms through which adenovirus manipulates host chromatin, we will understand new aspects of this ubiquitous virus and shed light on previously unknown aspects of chromatin biology.
Collapse
Affiliation(s)
- Kelsey L Lynch
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Linda R Gooding
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - David A Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| |
Collapse
|
17
|
Nacht AS, Ferrari R, Zaurin R, Scabia V, Carbonell-Caballero J, Le Dily F, Quilez J, Leopoldi A, Brisken C, Beato M, Vicent GP. C/EBPα mediates the growth inhibitory effect of progestins on breast cancer cells. EMBO J 2019; 38:e101426. [PMID: 31373033 DOI: 10.15252/embj.2018101426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 01/19/2023] Open
Abstract
Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome-wide approaches to show that progestins achieve this effect via a functional crosstalk with C/EBPα. Using ChIP-seq, we identify around 1,000 sites where C/EBPα binding precedes and helps binding of progesterone receptor (PR) in response to hormone. These regions exhibit epigenetic marks of active enhancers, and C/EBPα maintains an open chromatin conformation that facilitates loading of ligand-activated PR. Prior to hormone exposure, C/EBPα favors promoter-enhancer contacts that assure hormonal regulation of key genes involved in cell proliferation by facilitating binding of RAD21, YY1, and the Mediator complex. Knockdown of C/EBPα disrupts enhancer-promoter contacts and decreases the presence of these architectural proteins, highlighting its key role in 3D chromatin looping. Thus, C/EBPα fulfills a previously unknown function as a potential growth modulator in hormone-dependent breast cancer.
Collapse
Affiliation(s)
- A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Roser Zaurin
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Valentina Scabia
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - José Carbonell-Caballero
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Javier Quilez
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Alexandra Leopoldi
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Cathrin Brisken
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| |
Collapse
|
18
|
Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci 2019; 20:ijms20133315. [PMID: 31284509 PMCID: PMC6651528 DOI: 10.3390/ijms20133315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.
Collapse
|
19
|
H3K18Ac as a Marker of Cancer Progression and Potential Target of Anti-Cancer Therapy. Cells 2019; 8:cells8050485. [PMID: 31121824 PMCID: PMC6562857 DOI: 10.3390/cells8050485] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 02/07/2023] Open
Abstract
Acetylation and deacetylation are posttranslational modifications (PTMs) which affect the regulation of chromatin structure and its remodeling. Acetylation of histone 3 at lysine placed on position 18 (H3K18Ac) plays an important role in driving progression of many types of cancer, including breast, colon, lung, hepatocellular, pancreatic, prostate, and thyroid cancer. The aim of this review is to analyze and discuss the newest findings regarding the role of H3K18Ac and acetylation of other histones in carcinogenesis. We summarize the level of H3K18Ac in different cancer cell lines and analyze its association with patients’ outcomes, including overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS). Finally, we describe future perspectives of cancer therapeutic strategies based on H3K18 modifications.
Collapse
|
20
|
Sun F, Chronis C, Kronenberg M, Chen XF, Su T, Lay FD, Plath K, Kurdistani SK, Carey MF. Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods. Mol Cell 2019; 73:250-263.e5. [PMID: 30527662 PMCID: PMC6338517 DOI: 10.1016/j.molcel.2018.10.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/09/2018] [Accepted: 10/25/2018] [Indexed: 12/09/2022]
Abstract
Metazoan chromosomes are sequentially partitioned into topologically associating domains (TADs) and then into smaller sub-domains. One class of sub-domains, insulated neighborhoods, are proposed to spatially sequester and insulate the enclosed genes through self-association and chromatin looping. However, it has not been determined functionally whether promoter-enhancer interactions and gene regulation are broadly restricted to within these loops. Here, we employed published datasets from murine embryonic stem cells (mESCs) to identify insulated neighborhoods that confine promoter-enhancer interactions and demarcate gene regulatory regions. To directly address the functionality of these regions, we depleted estrogen-related receptor β (Esrrb), which binds the Mediator co-activator complex, to impair enhancers of genes within 222 insulated neighborhoods without causing mESC differentiation. Esrrb depletion reduces Mediator binding, promoter-enhancer looping, and expression of both nascent RNA and mRNA within the insulated neighborhoods without significantly affecting the flanking genes. Our data indicate that insulated neighborhoods represent functional regulons in mammalian genomes.
Collapse
MESH Headings
- Animals
- Binding Sites
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Mammalian
- Databases, Genetic
- Down-Regulation
- Enhancer Elements, Genetic
- Insulator Elements
- Mice
- Mouse Embryonic Stem Cells/physiology
- Promoter Regions, Genetic
- Protein Binding
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Transcription, Genetic
- Cohesins
Collapse
Affiliation(s)
- Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Michael Kronenberg
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Xiao-Fen Chen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Fides D Lay
- Department of Molecular, Cellular and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA.
| |
Collapse
|
21
|
Doerfler W, Weber S, Naumann A. Inheritable epigenetic response towards foreign DNA entry by mammalian host cells: a guardian of genomic stability. Epigenetics 2018; 13:1141-1153. [PMID: 30458693 DOI: 10.1080/15592294.2018.1549463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Apart from its well-documented role in long-term promoter silencing, the genome-wide distribution patterns of ~ 28 million methylated or unmethylated CpG dinucleotides, e. g. in the human genome, is in search of genetic functions. We have set out to study changes in the cellular CpG methylation profile upon introducing foreign DNA into mammalian cells. As stress factors served the genomic integration of foreign (viral or bacterial plasmid) DNA, virus infections or the immortalization of cells with Epstein Barr Virus (EBV). In all instances investigated, alterations in cellular CpG methylation and transcription profiles were observed to different degrees. In the case of adenovirus DNA integration in adenovirus type 12 (Ad12)-transformed hamster cells, the extensive changes in cellular CpG methylation persisted even after the complete loss of all transgenomic Ad12 DNA. Hence, stress-induced alterations in CpG methylation can be inherited independent of the continued presence of the transgenome. Upon virus infections, changes in cellular CpG methylation appear early after infection. In EBV immortalized as compared to control cells, CpG hypermethylation in the far-upstream region of the human FMR1 promoter decreased four-fold. We conclude that in the wake of cellular stress due to foreign DNA entry, preexisting CpG methylation patterns were altered, possibly at specific CpG dinucleotides. Frequently, transcription patterns were also affected. As a working concept, we view CpG methylation profiles in mammalian genomes as a guarding sensor for genomic stability under epigenetic control. As a caveat towards manipulations of cells with foreign DNA, such cells can no longer be considered identical to their un-manipulated counterparts.
Collapse
Affiliation(s)
- Walter Doerfler
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany.,b Institute of Genetics , Cologne University , Cologne , Germany
| | - Stefanie Weber
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany
| | - Anja Naumann
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany
| |
Collapse
|
22
|
Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters. J Virol 2018; 92:JVI.00805-18. [PMID: 29976669 PMCID: PMC6146688 DOI: 10.1128/jvi.00805-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 01/06/2023] Open
Abstract
Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 37:1095–1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters. How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated lacO array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly. IMPORTANCE Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 37:1095–1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.
Collapse
|
23
|
Enhancement of adenovirus infection and adenoviral vector-mediated gene delivery by bromodomain inhibitor JQ1. Sci Rep 2018; 8:11554. [PMID: 30068949 PMCID: PMC6070498 DOI: 10.1038/s41598-018-28421-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/20/2018] [Indexed: 01/08/2023] Open
Abstract
Adenovirus-based vectors are among the most commonly used platforms for gene delivery and gene therapy studies. One of the obstacles for potential application is dose-related toxicity. We show here that adenovirus infection and Ad-mediated gene delivery can be enhanced by inhibitors of bromodomain and extra-terminal (BET) family proteins. We showed that JQ1, but not its inactive enantiomer (−)-JQ1, dose-dependently promoted Ad infection and Ad-mediated gene delivery in both epithelial and lymphocyte cells. Given orally, JQ1 also enhanced transgene expression in a murine tumor model. Inhibitors of histone deacetylases (HDACi) are among the commonly reported small molecule compounds which enhance Ad-mediated gene delivery. We found that JQ1 treatment did not cause histone acetylation nor expression of Ad attachment receptor CAR. Instead, JQ1 treatment induced an increase in BRD4 association with CDK9, a subunit of P-TEFb of transcription elongation. Concurrently, we showed that CDK9 inhibition blocked Ad infection and JQ1 enhancement on the infection. The study exemplifies the potentials of BET inhibitors like JQ1 in oncolytic virotherapy.
Collapse
|
24
|
Adenovirus 5 E1A-Mediated Suppression of p53 via FUBP1. J Virol 2018; 92:JVI.00439-18. [PMID: 29743362 DOI: 10.1128/jvi.00439-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/02/2018] [Indexed: 12/31/2022] Open
Abstract
Far-upstream element (FUSE) binding protein 1 (FUBP1) was originally identified as a regulator of the oncogene c-Myc via binding to the FUSE within the c-Myc promoter and activating the expression of the gene. Recent studies have identified FUBP1 as a regulator of transcription, translation, and splicing via its DNA and RNA binding activities. Here we report the identification of FUBP1 as a novel binding partner of E1A. FUBP1 binds directly to E1A via the N terminus (residues 1 to 82) and conserved region 3 (residues 139 to 204) of adenovirus 5 E1A. The depletion of FUBP1 via short interfering RNAs (siRNA) reduces virus growth and drives the upregulation of the cellular stress response by activating the expression of p53-regulated genes. During infection, FUBP1 is relocalized within the nucleus, and it is recruited to viral promoters together with E1A while at the same time being lost from the FUSE upstream of the c-Myc promoter. The depletion of FUBP1 affects viral and cellular gene expression. Importantly, in FUBP1-depleted cells, p53-responsive genes are upregulated, p53 occupancy on target promoters is enhanced, and histone H3 lysine 9 is hyperacetylated. This is likely due to the loss of the FUBP1-mediated suppression of p53 DNA binding. We also observed that E1A stabilizes the FUBP1-p53 complex, preventing p53 promoter binding. Together, our results identify, for the first time, FUBP1 as a novel E1A binding protein that participates in aspects of viral replication and is involved in the E1A-mediated suppression of p53 function.IMPORTANCE Viral infection triggers innate cellular defense mechanisms that have evolved to block virus replication. To overcome this, viruses have counterevolved mechanisms that ensure that cellular defenses are either disarmed or not activated to guarantee successful replication. One of the key regulators of cellular stress is the tumor suppressor p53 that responds to a variety of cellular stress stimuli and safeguards the integrity of the genome. During infection, many viruses target the p53 pathway in order to deactivate it. Here we report that human adenovirus 5 coopts the cellular protein FUBP1 to prevent the activation of the p53 stress response pathway that would block viral replication. This finding adds to our understanding of p53 deactivation by adenovirus and highlights its importance in infection and innate immunity.
Collapse
|
25
|
Abstract
As obligate intracellular parasites, viruses are dependent on their infected hosts for survival. Consequently, viruses are under enormous selective pressure to utilize available cellular components and processes to their own advantage. As most, if not all, cellular activities are regulated at some level via protein interactions, host protein interaction networks are particularly vulnerable to viral exploitation. Indeed, viral proteins frequently target highly connected “hub” proteins to “hack” the cellular network, defining the molecular basis for viral control over the host. This widespread and successful strategy of network intrusion and exploitation has evolved convergently among numerous genetically distinct viruses as a result of the endless evolutionary arms race between pathogens and hosts. Here we examine the means by which a particularly well-connected viral hub protein, human adenovirus E1A, compromises and exploits the vulnerabilities of eukaryotic protein interaction networks. Importantly, these interactions identify critical regulatory hubs in the human proteome and help define the molecular basis of their function.
Collapse
|
26
|
Avgousti DC, Della Fera AN, Otter CJ, Herrmann C, Pancholi NJ, Weitzman MD. Adenovirus Core Protein VII Downregulates the DNA Damage Response on the Host Genome. J Virol 2017; 91:e01089-17. [PMID: 28794020 PMCID: PMC5625504 DOI: 10.1128/jvi.01089-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
Viral manipulation of cellular proteins allows viruses to suppress host defenses and generate infectious progeny. Due to the linear double-stranded DNA nature of the adenovirus genome, the cellular DNA damage response (DDR) is considered a barrier to successful infection. The adenovirus genome is packaged with protein VII, a virally encoded histone-like core protein that is suggested to protect incoming viral genomes from detection by the cellular DNA damage machinery. We showed that protein VII localizes to host chromatin during infection, leading us to hypothesize that protein VII may affect DNA damage responses on the cellular genome. Here we show that protein VII at cellular chromatin results in a significant decrease in accumulation of phosphorylated H2AX (γH2AX) following irradiation, indicating that protein VII inhibits DDR signaling. The oncoprotein SET was recently suggested to modulate the DDR by affecting access of repair proteins to chromatin. Since protein VII binds SET, we investigated a role for SET in DDR inhibition by protein VII. We show that knockdown of SET partially rescues the protein VII-induced decrease in γH2AX accumulation on the host genome, suggesting that SET is required for inhibition. Finally, we show that knockdown of SET also allows ATM to localize to incoming viral genomes bound by protein VII during infection with a mutant lacking early region E4. Together, our data suggest that the protein VII-SET interaction contributes to DDR evasion by adenovirus. Our results provide an additional example of a strategy used by adenovirus to abrogate the host DDR and show how viruses can modify cellular processes through manipulation of host chromatin.IMPORTANCE The DNA damage response (DDR) is a cellular network that is crucial for maintaining genome integrity. DNA viruses replicating in the nucleus challenge the resident genome and must overcome cellular responses, including the DDR. Adenoviruses are prevalent human pathogens that can cause a multitude of diseases, such as respiratory infections and conjunctivitis. Here we describe how a small adenovirus core protein that localizes to host chromatin during infection can globally downregulate the DDR. Our study focuses on key players in the damage signaling pathway and highlights how viral manipulation of chromatin may influence access of DDR proteins to the host genome.
Collapse
Affiliation(s)
- Daphne C Avgousti
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Clayton J Otter
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christin Herrmann
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Neha J Pancholi
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| |
Collapse
|
27
|
Nguyen AH, Elliott IA, Wu N, Matsumura C, Vogelauer M, Attar N, Dann A, Ghukasyan R, Toste PA, Patel SG, Williams JL, Li L, Dawson DW, Radu C, Kurdistani SK, Donahue TR. Histone deacetylase inhibitors provoke a tumor supportive phenotype in pancreatic cancer associated fibroblasts. Oncotarget 2017; 8:19074-19088. [PMID: 27894105 PMCID: PMC5386671 DOI: 10.18632/oncotarget.13572] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
Although histone deacetylase inhibitors (HDACi) are a promising class of anti-cancer drugs, thus far, they have been unsuccessful in early phase clinical trials for pancreatic ductal adenocarcinoma (PDAC). One potential reason for their poor efficacy is the tumor stroma, where cancer-associated fibroblasts (CAFs) are a prominent cell type and a source of resistance to cancer therapies. Here, we demonstrate that stromal fibroblasts contribute to the poor efficacy of HDACi's in PDAC. HDACi-treated fibroblasts show increased biological aggressiveness and are characterized by increased secretion of pro-inflammatory tumor-supportive cytokines and chemokines. We find that HDAC2 binds to the enhancer and promoter regions of pro-inflammatory genes specifically in CAFs and in silico analysis identified AP-1 to be the most frequently associated transcription factor bound in these regions. Pharmacologic inhibition of pathways upstream of AP-1 suppresses the HDACi-induced inflammatory gene expression and tumor-supportive responses in fibroblasts. Our findings demonstrate that the combination of HDACi's with chemical inhibitors of the AP-1 signaling pathway attenuate the inflammatory phenotype of fibroblasts and may improve the efficacy of HDACi in PDAC and, potentially, in other solid tumors rich in stroma.
Collapse
Affiliation(s)
- Andrew H Nguyen
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Irmina A Elliott
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Nanping Wu
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Cynthia Matsumura
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Amanda Dann
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Razmik Ghukasyan
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Paul A Toste
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Sanjeet G Patel
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jennifer L Williams
- Department of Surgery, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Luyi Li
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Caius Radu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Timothy R Donahue
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| |
Collapse
|
28
|
Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res 2017; 45:4493-4506. [PMID: 28158860 PMCID: PMC5416754 DOI: 10.1093/nar/gkx058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 01/25/2017] [Indexed: 01/21/2023] Open
Abstract
Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. Here, we show that most Ribi gene promoters also contain binding sites for one or more General Regulatory Factors (GRFs), most frequently Abf1 and Reb1, and that these factors are enriched in vivo at Ribi promoters. Abf1/Reb1/Tbf1 promoter association was required for full Ribi gene expression in rich medium and for its modulation in response to glucose starvation, characterized by a rapid drop followed by slow recovery. Such a response did not entail changes in Abf1 occupancy, but it was paralleled by a quick increase, followed by slow decrease, in Rpd3L histone deacetylase occupancy. Remarkably, Abf1 site disruption also abolished Rpd3L complex recruitment in response to starvation. Extensive mutational analysis of the DBP7 promoter revealed a complex interplay of Tbf1 sites, PAC and RRPE in the transcriptional regulation of this Ribi gene. Our observations point to GRFs as new multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions.
Collapse
Affiliation(s)
- Maria Cristina Bosio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Beatrice Fermi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gloria Spagnoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Elisabetta Levati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Ludmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roberto Ferrari
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| |
Collapse
|
29
|
Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals. Mol Cell 2017; 67:594-607.e4. [PMID: 28735899 DOI: 10.1016/j.molcel.2017.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/12/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023]
Abstract
Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C, or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.
Collapse
Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
30
|
Huang C, Su T, Xue Y, Cheng C, Lay FD, McKee RA, Li M, Vashisht A, Wohlschlegel J, Novitch BG, Plath K, Kurdistani SK, Carey M. Cbx3 maintains lineage specificity during neural differentiation. Genes Dev 2017; 31:241-246. [PMID: 28270516 PMCID: PMC5358721 DOI: 10.1101/gad.292169.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/27/2017] [Indexed: 02/05/2023]
Abstract
Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.
Collapse
Affiliation(s)
- Chengyang Huang
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Trent Su
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Yong Xue
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Fides D Lay
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Robin A McKee
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Meiyang Li
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Ajay Vashisht
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Bennett G Novitch
- Department of Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Michael Carey
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| |
Collapse
|
31
|
Frost JR, Olanubi O, Cheng SKH, Soriano A, Crisostomo L, Lopez A, Pelka P. The interaction of adenovirus E1A with the mammalian protein Ku70/XRCC6. Virology 2016; 500:11-21. [PMID: 27769014 DOI: 10.1016/j.virol.2016.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 11/30/2022]
Abstract
Human adenovirus infects terminally differentiated cells and to replicate it must induce S-phase. The chief architects that drive adenovirus-infected cells into S-phase are the E1A proteins, with 5 different isoforms expressed during infection. E1A remodels the infected cell by associating with cellular factors and modulating their activity. The C-terminus of E1A is known to bind to only a handful of proteins. We have identified a novel E1A C-terminus binding protein, Ku70 (XRCC6), which was found to bind directly within the CR4 of E1A from human adenovirus type 5. Depletion of Ku70 reduced virus growth, possibly by activating the DNA damage response pathway. Ku70 was found to localize to viral replication centers and associate with the viral genome. Ku70 was also recruited to cellular cell cycle regulated promoters following viral infection. Our study has identified, for the first time, Ku70 as a novel E1A-binding protein which affects virus life cycle.
Collapse
Affiliation(s)
- Jasmine Rae Frost
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2
| | - Oladunni Olanubi
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2
| | | | - Andrea Soriano
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2
| | - Leandro Crisostomo
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2
| | - Alennie Lopez
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB, Canada, R3T 2N2.
| |
Collapse
|
32
|
Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 509] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
Collapse
Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
| |
Collapse
|
33
|
Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells. Leukemia 2016; 30:2302-2311. [PMID: 27211267 PMCID: PMC5143163 DOI: 10.1038/leu.2016.139] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/24/2016] [Accepted: 05/04/2016] [Indexed: 12/16/2022]
Abstract
The transcription factor CREB (cAMP Response-Element Binding Protein) is overexpressed in the majority of acute myeloid leukemia (AML) patients, and this is associated with a worse prognosis. Previous work revealed that CREB overexpression augmented AML cell growth, while CREB knockdown disrupted key AML cell functions in vitro. In contrast, CREB knockdown had no effect on long-term hematopoietic stem cell activity in mouse transduction/transplantation assays. Together, these studies position CREB as a promising drug target for AML. To test this concept, a small molecule inhibitor of CREB, XX-650-23, was developed. This molecule blocks a critical interaction between CREB and its required co-activator CBP (CREB Binding Protein), leading to disruption of CREB-driven gene expression. Inhibition of CBP-CREB interaction induced apoptosis and cell-cycle arrest in AML cells, and prolonged survival in vivo in mice injected with human AML cells. XX-650-23 had little toxicity on normal human hematopoietic cells and tissues in mice. To understand the mechanism of XX-650-23, we performed RNA-seq, ChIP-seq and Cytometry Time of Flight with human AML cells. Our results demonstrate that small molecule inhibition of CBP-CREB interaction mostly affects apoptotic, cell-cycle and survival pathways, which may represent a novel approach for AML therapy.
Collapse
|
34
|
Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med 2016; 8:54. [PMID: 27146673 PMCID: PMC4857420 DOI: 10.1186/s13073-016-0305-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genetic origins of chemotherapy resistance are well established; however, the role of epigenetics in drug resistance is less well understood. To investigate mechanisms of drug resistance, we performed systematic genetic, epigenetic, and transcriptomic analyses of an alkylating agent-sensitive murine lymphoma cell line and a series of resistant lines derived by drug dose escalation. Methods Dose escalation of the alkylating agent mafosfamide was used to create a series of increasingly drug-resistant mouse Burkitt’s lymphoma cell lines. Whole genome sequencing, DNA microarrays, reduced representation bisulfite sequencing, and chromatin immunoprecipitation sequencing were used to identify alterations in DNA sequence, mRNA expression, CpG methylation, and H3K27me3 occupancy, respectively, that were associated with increased resistance. Results Our data suggest that acquired resistance cannot be explained by genetic alterations. Based on integration of transcriptional profiles with transcription factor binding data, we hypothesize that resistance is driven by epigenetic plasticity. We observed that the resistant cells had H3K27me3 and DNA methylation profiles distinct from those of the parental lines. Moreover, we observed DNA methylation changes in the promoters of genes regulated by E2a and members of the polycomb repressor complex 2 (PRC2) and differentially expressed genes were enriched for targets of E2a. The integrative analysis considering H3K27me3 further supported a role for PRC2 in mediating resistance. By integrating our results with data from the Immunological Genome Project (Immgen.org), we showed that these transcriptional changes track the B-cell maturation axis. Conclusions Our data suggest a novel mechanism of drug resistance in which E2a and PRC2 drive changes in the B-cell epigenome; these alterations attenuate alkylating agent treatment-induced apoptosis. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0305-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Colin Flinders
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Larry Lam
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Roberto Ferrari
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Sorel Fitz-Gibbon
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Pao-Yang Chen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Michael Thompson
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Heather Christofk
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - David B Agus
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Daniel Ruderman
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Parag Mallick
- Canary Center, Stanford University, Palo Alto, CA, 94305, USA. .,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
35
|
Ornelles DA, Gooding LR, Dickherber ML, Policard M, Garnett-Benson C. Limited but durable changes to cellular gene expression in a model of latent adenovirus infection are reflected in childhood leukemic cell lines. Virology 2016; 494:67-77. [PMID: 27085068 PMCID: PMC4946252 DOI: 10.1016/j.virol.2016.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
Mucosal lymphocytes support latent infections of species C adenoviruses. Because infected lymphocytes resist re-infection with adenovirus, we sought to identify changes in cellular gene expression that could inhibit the infectious process. The expression of over 30,000 genes was evaluated by microarray in persistently infected B-and T-lymphocytic cells. BBS9, BNIP3, BTG3, CXADR, SLFN11 and SPARCL1 were the only genes differentially expressed between mock and infected B cells. Most of these genes are associated with oncogenesis or cancer progression. Histone deacetylase and DNA methyltransferase inhibitors released the repression of some of these genes. Cellular and viral gene expression was compared among leukemic cell lines following adenovirus infection. Childhood leukemic B-cell lines resist adenovirus infection and also show reduced expression of CXADR and SPARCL. Thus adenovirus induces limited changes to infected B-cell lines that are similar to changes observed in childhood leukemic cell lines.
Collapse
Affiliation(s)
- D A Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - L R Gooding
- Emory University School of Medicine, Department of Microbiology and Immunology, Atlanta, GA 30322, United States
| | - M L Dickherber
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - M Policard
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - C Garnett-Benson
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States.
| |
Collapse
|
36
|
Pradhan SK, Su T, Yen L, Jacquet K, Huang C, Côté J, Kurdistani SK, Carey MF. EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation. Mol Cell 2015; 61:27-38. [PMID: 26669263 DOI: 10.1016/j.molcel.2015.10.039] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/28/2015] [Accepted: 10/26/2015] [Indexed: 11/15/2022]
Abstract
Gene activation in metazoans is accompanied by the presence of histone variants H2AZ and H3.3 within promoters and enhancers. It is not known, however, what protein deposits H3.3 into chromatin or whether variant chromatin plays a direct role in gene activation. Here we show that chromatin containing acetylated H2AZ and H3.3 stimulates transcription in vitro. Analysis of the Pol II pre-initiation complex on immobilized chromatin templates revealed that the E1A binding protein p400 (EP400) was bound preferentially to and required for transcription stimulation by acetylated double-variant chromatin. EP400 also stimulated H2AZ/H3.3 deposition into promoters and enhancers and influenced transcription in vivo at a step downstream of the Mediator complex. EP400 efficiently exchanged recombinant histones H2A and H3.1 with H2AZ and H3.3, respectively, in a chromatin- and ATP-stimulated manner in vitro. Our data reveal that EP400 deposits H3.3 into chromatin alongside H2AZ and contributes to gene regulation after PIC assembly.
Collapse
Affiliation(s)
- Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Linda Yen
- The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA
| | - Karine Jacquet
- Laval University Cancer Research Center, CHU de Québec Research Center-Oncology, Hôtel-Dieu de Québec, 9 McMahon Street, Quebec City, QC G1R 2J6, Canada
| | - Chengyang Huang
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec Research Center-Oncology, Hôtel-Dieu de Québec, 9 McMahon Street, Quebec City, QC G1R 2J6, Canada
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA; The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA; The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA.
| |
Collapse
|
37
|
Radko S, Jung R, Olanubi O, Pelka P. Effects of Adenovirus Type 5 E1A Isoforms on Viral Replication in Arrested Human Cells. PLoS One 2015; 10:e0140124. [PMID: 26448631 PMCID: PMC4598095 DOI: 10.1371/journal.pone.0140124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/21/2015] [Indexed: 11/22/2022] Open
Abstract
Human adenovirus has evolved to infect and replicate in terminally differentiated human epithelial cells, predominantly those within the airway, the gut, or the eye. To overcome the block to viral DNA replication present in these cells, the virus expresses the Early 1A proteins (E1A). These immediate early proteins drive cells into S-phase and induce expression of all other viral early genes. During infection, several E1A isoforms are expressed with proteins of 289, 243, 217, 171, and 55 residues being present for human adenovirus type 5. Here we examine the contribution that the two largest E1A isoforms make to the viral life cycle in growth-arrested normal human fibroblasts. Viruses that express E1A289R were found to replicate better than those that do not express this isoform. Importantly, induction of several viral genes was delayed in a virus expressing E1A243R, with several viral structural proteins undetectable by western blot. We also highlight the changes in E1A isoforms detected during the course of viral infection. Furthermore, we show that viral DNA replication occurs more efficiently, leading to higher number of viral genomes in cells infected with viruses that express E1A289R. Finally, induction of S-phase specific genes differs between viruses expressing different E1A isoforms, with those having E1A289R leading to, generally, earlier activation of these genes. Overall, we provide an overview of adenovirus replication using modern molecular biology approaches and further insights into the contribution that E1A isoforms make to the life cycle of human adenovirus in arrested human fibroblasts.
Collapse
Affiliation(s)
- Sandi Radko
- Department of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Buller Building Room 427, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Richard Jung
- Department of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Buller Building Room 427, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Oladunni Olanubi
- Department of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Buller Building Room 427, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Buller Building Room 427, Winnipeg, Manitoba, R3T 2N2, Canada
- * E-mail:
| |
Collapse
|
38
|
Stabilization of SIRT7 deacetylase by viral oncoprotein HBx leads to inhibition of growth restrictive RPS7 gene and facilitates cellular transformation. Sci Rep 2015; 5:14806. [PMID: 26442981 PMCID: PMC4595800 DOI: 10.1038/srep14806] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/09/2015] [Indexed: 02/06/2023] Open
Abstract
Sirtuin-7 (SIRT7) deacetylase exhibits a high selectivity for acetylated H3K18 and has been implicated in the maintenance of malignant phenotype. However, it remains unclear if SIRT7 and H3K18ac play a role in the tumorigenic program driven by oncogenic viruses. We show that ectopically expressed HBx oncoprotein of hepatitis B virus promoted intracellular stability of SIRT7 by salvaging it from ubiquitin-mediated proteasomal degradation. HBx-dependent accumulation of SIRT7 favored H3K18 deacetylation and down-regulated the small ribosomal protein gene, RPS7, involved in cell death and DNA damage response. HBx facilitated the recruitment of SIRT7 to RPS7 promoter thus impeding H3K18ac occupancy and hindering RPS7 transcription. The antagonistic relationship between SIRT7 and RPS7 was also observed in the HBx transgenic mice, where elevated levels of SIRT7 protein were coincident with low levels of H3K18ac and RPS7. Strikingly, inhibition of cellular deubiquitinase activity restored RPS7 gene transcription. Further, depletion of endogenous SIRT7 led to decreased cell viability and transformation. The biological relevance of RPS7 suppression by HBx-SIRT7 axis was evident from ectopic expression of RPS7 which attenuated clonogenicity of cells. Thus, our findings suggest that SIRT7 is a critical regulator of HBx-driven oncogenic program, through its antagonistic impact on growth restrictive ribosomal protein RPS7.
Collapse
|
39
|
Ying B, Toth K, Spencer JF, Aurora R, Wold WSM. Transcriptome sequencing and development of an expression microarray platform for liver infection in adenovirus type 5-infected Syrian golden hamsters. Virology 2015; 485:305-12. [PMID: 26319212 PMCID: PMC4619110 DOI: 10.1016/j.virol.2015.07.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/03/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
The Syrian golden hamster is an attractive animal for research on infectious diseases and other diseases. We report here the sequencing, assembly, and annotation of the Syrian hamster transcriptome. We include transcripts from ten pooled tissues from a naïve hamster and one stimulated with lipopolysaccharide. Our data set identified 42,707 non-redundant transcripts, representing 34,191 unique genes. Based on the transcriptome data, we generated a custom microarray and used this new platform to investigate the transcriptional response in the Syrian hamster liver following intravenous adenovirus type 5 (Ad5) infection. We found that Ad5 infection caused a massive change in regulation of liver transcripts, with robust up-regulation of genes involved in the antiviral response, indicating that the innate immune response functions in the host defense against Ad5 infection of the liver. The data and novel platforms developed in this study will facilitate further development of this important animal model. Syrian hamster transcriptome; 42,707 transcripts representing 34,191 unique genes Syrian hamster custom expression microarray platform Ad5 intravenous infection of the Syrian hamster liver Ad5 upregulation of hamster liver genes involved in innate antiviral response.
Collapse
Affiliation(s)
- Baoling Ying
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO 63104, United States
| | - Karoly Toth
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO 63104, United States
| | - Jacqueline F Spencer
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO 63104, United States
| | - Rajeev Aurora
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO 63104, United States
| | - William S M Wold
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO 63104, United States
| |
Collapse
|
40
|
Marazzi I, Garcia-Sastre A. Interference of viral effector proteins with chromatin, transcription, and the epigenome. Curr Opin Microbiol 2015; 26:123-9. [PMID: 26232586 DOI: 10.1016/j.mib.2015.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Pathogens exploit cellular functions to create an environment conducive to their persistence and propagation. Viruses and bacteria express effector-proteins or virulence factors, known to interfere at the molecular level with regulatory 'checkpoints' of numerous physiological events in the cell. A newly prominent area of research is the identification of pathogenic effector proteins that function on the host chromatin, their subversion/interference with chromatin regulatory processes, the short/long/heritable effects on the infected cell and the ultimate consequence of their expression at the organismal level.
Collapse
Affiliation(s)
- Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, NY, USA.
| |
Collapse
|
41
|
Abstract
DNA tumor viruses including members of the polyomavirus, adenovirus, papillomavirus, and herpes virus families are presently the subject of intense interest with respect to the role that epigenetics plays in control of the virus life cycle and the transformation of a normal cell to a cancer cell. To date, these studies have primarily focused on the role of histone modification, nucleosome location, and DNA methylation in regulating the biological consequences of infection. Using a wide variety of strategies and techniques ranging from simple ChIP to ChIP-chip and ChIP-seq to identify histone modifications, nuclease digestion to genome wide next generation sequencing to identify nucleosome location, and bisulfite treatment to MeDIP to identify DNA methylation sites, the epigenetic regulation of these viruses is slowly becoming better understood. While the viruses may differ in significant ways from each other and cellular chromatin, the role of epigenetics appears to be relatively similar. Within the viral genome nucleosomes are organized for the expression of appropriate genes with relevant histone modifications particularly histone acetylation. DNA methylation occurs as part of the typical gene silencing during latent infection by herpesviruses. In the simple tumor viruses like the polyomaviruses, adenoviruses, and papillomaviruses, transformation of the cell occurs via integration of the virus genome such that the virus's normal regulation is disrupted. This results in the unregulated expression of critical viral genes capable of redirecting cellular gene expression. The redirected cellular expression is a consequence of either indirect epigenetic regulation where cellular signaling or transcriptional dysregulation occurs or direct epigenetic regulation where epigenetic cofactors such as histone deacetylases are targeted. In the more complex herpersviruses transformation is a consequence of the expression of the viral latency proteins and RNAs which again can have either a direct or indirect effect on epigenetic regulation of cellular expression. Nevertheless, many questions still remain with respect to the specific mechanisms underlying epigenetic regulation of the viruses and transformation.
Collapse
|
42
|
Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev 2015; 29:350-5. [PMID: 25691465 PMCID: PMC4335291 DOI: 10.1101/gad.256255.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Heterochromatin stimulates the binding of Ino80C in vitro and in vivo. Our data reveal that Ino80C serves as a general silencing complex that restricts transcription to gene units in euchromatin.
Collapse
Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Jason Gehrke
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Benjamin G Kuryan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Tasuku Kitada
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA;
| |
Collapse
|
43
|
Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. eLife 2015; 4:e06205. [PMID: 25848745 PMCID: PMC4412109 DOI: 10.7554/elife.06205] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/02/2015] [Indexed: 12/17/2022] Open
Abstract
Methylation of cytosines (5(me)C) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here, we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 shows an increase of relative 5(me)C levels at the transcription start site and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo.
Collapse
Affiliation(s)
- Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - William A Pastor
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Barbara Montanini
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, Laboratory of Functional Genomics and Protein Engineering, Parma, Italy
| | - Kevin Nee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Roberto Ferrari
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Kai Fu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Giancarlo Bonora
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Simone Ottonello
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, Laboratory of Functional Genomics and Protein Engineering, Parma, Italy
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
| |
Collapse
|
44
|
Borna disease virus phosphoprotein modulates epigenetic signaling in neurons to control viral replication. J Virol 2015; 89:5996-6008. [PMID: 25810554 DOI: 10.1128/jvi.00454-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/17/2015] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED Understanding the modalities of interaction of neurotropic viruses with their target cells represents a major challenge that may improve our knowledge of many human neurological disorders for which viral origin is suspected. Borna disease virus (BDV) represents an ideal model to analyze the molecular mechanisms of viral persistence in neurons and its consequences for neuronal homeostasis. It is now established that BDV ensures its long-term maintenance in infected cells through a stable interaction of viral components with the host cell chromatin, in particular, with core histones. This has led to our hypothesis that such an interaction may trigger epigenetic changes in the host cell. Here, we focused on histone acetylation, which plays key roles in epigenetic regulation of gene expression, notably for neurons. We performed a comparative analysis of histone acetylation patterns of neurons infected or not infected by BDV, which revealed that infection decreases histone acetylation on selected lysine residues. We showed that the BDV phosphoprotein (P) is responsible for these perturbations, even when it is expressed alone independently of the viral context, and that this action depends on its phosphorylation by protein kinase C. We also demonstrated that BDV P inhibits cellular histone acetyltransferase activities. Finally, by pharmacologically manipulating cellular acetylation levels, we observed that inhibiting cellular acetyl transferases reduces viral replication in cell culture. Our findings reveal that manipulation of cellular epigenetics by BDV could be a means to modulate viral replication and thus illustrate a fascinating example of virus-host cell interaction. IMPORTANCE Persistent DNA viruses often subvert the mechanisms that regulate cellular chromatin dynamics, thereby benefitting from the resulting epigenetic changes to create a favorable milieu for their latent and persistent states. Here, we reasoned that Borna disease virus (BDV), the only RNA virus known to durably persist in the nucleus of infected cells, notably neurons, might employ a similar mechanism. In this study, we uncovered a novel modality of virus-cell interaction in which BDV phosphoprotein inhibits cellular histone acetylation by interfering with histone acetyltransferase activities. Manipulation of cellular histone acetylation is accompanied by a modulation of viral replication, revealing a perfect adaptation of this "ancient" virus to its host that may favor neuronal persistence and limit cellular damage.
Collapse
|
45
|
Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerényi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J 2015; 34:759-77. [PMID: 25564442 PMCID: PMC4369313 DOI: 10.15252/embj.201490542] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic marks. Our data suggest that, rather than recruiting corepressors to enhancers, Scl prevents ectopic cardiogenesis by occupying enhancers that cardiac factors, such as Gata4 and Hand1, use for gene activation. Although hematopoietic Gata factors bind with Scl to both activated and repressed genes, they are dispensable for cardiac repression, but necessary for activating genes that enable hematopoietic stem/progenitor cell development. These results suggest that a unique subset of enhancers in lineage-specific genes that are accessible for regulators of opposing fates during the time of the fate decision provide a platform where the divergence of mutually exclusive fates is orchestrated.
Collapse
Affiliation(s)
- Tõnis Org
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Dan Duan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Roberto Ferrari
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Amelie Montel-Hagen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Ben Van Handel
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Marc A Kerényi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Yuko Fujiwara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Hanna Ka Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| |
Collapse
|
46
|
Ferrari R, Gou D, Jawdekar G, Johnson SA, Nava M, Su T, Yousef AF, Zemke NR, Pellegrini M, Kurdistani SK, Berk AJ. Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Cell Host Microbe 2014; 16:663-76. [PMID: 25525796 DOI: 10.1016/j.chom.2014.10.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/25/2014] [Accepted: 09/07/2014] [Indexed: 12/27/2022]
Abstract
Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. These repressing p300-e1a-RB1 complexes specifically interact with host genes that have unusually high p300 association within the gene body. The TGF-β, TNF-, and interleukin-signaling pathway components are enriched among such p300-targeted genes. The p300-e1a-RB1 complex condenses chromatin in a manner dependent on HDAC activity, p300 lysine acetylase activity, the p300 bromodomain, and RB K873/K874 and e1a K239 acetylation to repress host genes that would otherwise inhibit productive virus infection. Thus, adenovirus employs e1a to repress host genes that interfere with viral replication.
Collapse
Affiliation(s)
- Roberto Ferrari
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Dawei Gou
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Microbiology, Immunology and Molecular Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Gauri Jawdekar
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Sarah A Johnson
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Miguel Nava
- Department of Microbiology, Immunology and Molecular Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Trent Su
- Department of Biological Chemistry, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Ahmed F Yousef
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Nathan R Zemke
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Matteo Pellegrini
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Molecular, Cellular, and Developmental Biology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Siavash K Kurdistani
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Biological Chemistry, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Pathology and Laboratory of Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA
| | - Arnold J Berk
- Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Microbiology, Immunology and Molecular Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA.
| |
Collapse
|
47
|
Unabated adenovirus replication following activation of the cGAS/STING-dependent antiviral response in human cells. J Virol 2014; 88:14426-39. [PMID: 25297994 DOI: 10.1128/jvi.02608-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED The cGAS/STING DNA sensing complex has recently been established as a predominant pathogen recognition receptor (PRR) for DNA-directed type I interferon (IFN) innate immune activation. Using replication-defective adenovirus vectors and replication-competent wild-type adenovirus, we have modeled the influence of the cGAS/STING cascade in permissive human cell lines (A549, HeLa, ARPE19, and THP1). Wild-type adenovirus induced efficient early activation of the cGAS/STING cascade in a cell-specific manner. In all responsive cell lines, cGAS/STING short hairpin RNA (shRNA) knockdown resulted in a loss of TBK1 and interferon response factor 3 (IRF3) activation, a lack of beta interferon transcript induction, loss of interferon-dependent STAT1 activation, and diminished induction of interferon-stimulated genes (ISGs). Adenoviruses that infect through the coxsackievirus-adenovirus receptor (CAR) (Ad2 and Ad5) and the CD46 (Ad35) and desmoglein-2 (Ad7) viral receptors all induce the cGAS/STING/TBK1/IRF3 cascade. The magnitude of the IRF3/IFN/ISG antiviral response was strongly influenced by serotype, with Ad35>Ad7>Ad2. For each serotype, no enhancement of viral DNA replication or virus production occurred in cGAS or STING shRNA-targeted cell line pools. We found no replication advantage in permissive cell lines that do not trigger the cGAS/STING cascade following infection. The cGAS/STING/TBK1/IRF3 cascade was not a direct target of viral antihost strategies, and we found no evidence that Ad stimulation of the cGAS/STING DNA response had an impact on viral replication efficiency. IMPORTANCE This study shows for the first time that the cGAS DNA sensor directs a dominant IRF3/IFN/ISG antiviral response to adenovirus in human cell lines. Activation of cGAS occurs with viruses that infect through different high-affinity receptors (CAR, CD46, and desmoglein-2), and the magnitude of the cGAS/STING DNA response cascade is influenced by serotype-specific functions. Furthermore, activation of the cGAS cascade occurred in a cell-specific manner. Activation of the cGAS/STING response did not impact viral replication, and viral immune evasion strategies did not target the cGAS/STING/TBK1/IRF3 cascade. These studies provide novel insight into the early innate recognition response to adenovirus.
Collapse
|
48
|
Adenovirus E1A targets the DREF nuclear factor to regulate virus gene expression, DNA replication, and growth. J Virol 2014; 88:13469-81. [PMID: 25210186 DOI: 10.1128/jvi.02538-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The adenovirus E1A gene is the first gene expressed upon viral infection. E1A remodels the cellular environment to maximize permissivity for viral replication. E1A is also the major transactivator of viral early gene expression and a coregulator of a large number of cellular genes. E1A carries out its functions predominantly by binding to cellular regulatory proteins and altering their activities. The unstructured nature of E1A enables it to bind to a large variety of cellular proteins and form new molecular complexes with novel functions. The C terminus of E1A is the least-characterized region of the protein, with few known binding partners. Here we report the identification of cellular factor DREF (ZBED1) as a novel and direct binding partner of E1A. Our studies identify a dual role for DREF in the viral life cycle. DREF contributes to activation of gene expression from all viral promoters early in infection. Unexpectedly, it also functions as a growth restriction factor for adenovirus as knockdown of DREF enhances virus growth and increases viral genome copy number late in the infection. We also identify DREF as a component of viral replication centers. E1A affects the subcellular distribution of DREF within PML bodies and enhances DREF SUMOylation. Our findings identify DREF as a novel E1A C terminus binding partner and provide evidence supporting a role for DREF in viral replication. IMPORTANCE This work identifies the putative transcription factor DREF as a new target of the E1A oncoproteins of human adenovirus. DREF was found to primarily localize with PML nuclear bodies in uninfected cells and to relocalize into virus replication centers during infection. DREF was also found to be SUMOylated, and this was enhanced in the presence of E1A. Knockdown of DREF reduced the levels of viral transcripts detected at 20 h, but not at 40 h, postinfection, increased overall virus yield, and enhanced viral DNA replication. DREF was also found to localize to viral promoters during infection together with E1A. These results suggest that DREF contributes to activation of viral gene expression. However, like several other PML-associated proteins, DREF also appears to function as a growth restriction factor for adenovirus infection.
Collapse
|
49
|
Liu X, Zhao L, Yang Y, Bode L, Huang H, Liu C, Huang R, Zhang L, Wang X, Zhang L, Liu S, Zhou J, Li X, He T, Cheng Z, Xie P. Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells. Virology 2014; 464-465:196-205. [PMID: 25086498 PMCID: PMC7112117 DOI: 10.1016/j.virol.2014.06.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/23/2014] [Accepted: 06/30/2014] [Indexed: 12/18/2022]
Abstract
Background Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. BDV infection affected the expression of many transcription factors and several HATs and HDACs.
Collapse
Affiliation(s)
- Xia Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Neurology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, 200240, China
| | - Libo Zhao
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Neurology, The Third People's Hospital of Chongqing, 400014, China
| | - Yongtao Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Liv Bode
- Bornavirus Research Group affiliated to the Free University of Berlin, Berlin, Germany
| | - Hua Huang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Chengyu Liu
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Rongzhong Huang
- Department of Rehabilitative Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Liang Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Xiao Wang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Lujun Zhang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Siwen Liu
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Jingjing Zhou
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China
| | - Xin Li
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Tieming He
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Zhongyi Cheng
- Advanced Institute of Translational Medicine, Tongji University, Shanghai, 200092, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
50
|
|