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Vogt M, Dudvarski Stankovic N, Cruz Garcia Y, Hofstetter J, Schneider K, Kuybu F, Hauck T, Adhikari B, Hamann A, Rocca Y, Grysczyk L, Martin B, Gebhardt-Wolf A, Wiegering A, Diefenbacher M, Gasteiger G, Knapp S, Saur D, Eilers M, Rosenfeldt M, Erhard F, Vos SM, Wolf E. Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2. Gut 2024:gutjnl-2023-331519. [PMID: 38821858 DOI: 10.1136/gutjnl-2023-331519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/15/2024] [Indexed: 06/02/2024]
Abstract
OBJECTIVE The hallmark oncogene MYC drives the progression of most tumours, but direct inhibition of MYC by a small-molecule drug has not reached clinical testing. MYC is a transcription factor that depends on several binding partners to function. We therefore explored the possibility of targeting MYC via its interactome in pancreatic ductal adenocarcinoma (PDAC). DESIGN To identify the most suitable targets among all MYC binding partners, we constructed a targeted shRNA library and performed screens in cultured PDAC cells and tumours in mice. RESULTS Unexpectedly, many MYC binding partners were found to be important for cultured PDAC cells but dispensable in vivo. However, some were also essential for tumours in their natural environment and, among these, the ATPases RUVBL1 and RUVBL2 ranked first. Degradation of RUVBL1 by the auxin-degron system led to the arrest of cultured PDAC cells but not untransformed cells and to complete tumour regression in mice, which was preceded by immune cell infiltration. Mechanistically, RUVBL1 was required for MYC to establish oncogenic and immunoevasive gene expression identifying the RUVBL1/2 complex as a druggable vulnerability in MYC-driven cancer. CONCLUSION One implication of our study is that PDAC cell dependencies are strongly influenced by the environment, so genetic screens should be performed in vitro and in vivo. Moreover, the auxin-degron system can be applied in a PDAC model, allowing target validation in living mice. Finally, by revealing the nuclear functions of the RUVBL1/2 complex, our study presents a pharmaceutical strategy to render pancreatic cancers potentially susceptible to immunotherapy.
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Affiliation(s)
- Markus Vogt
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Nevenka Dudvarski Stankovic
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Yiliam Cruz Garcia
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Katharina Schneider
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Filiz Kuybu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Theresa Hauck
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bikash Adhikari
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Anton Hamann
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Yamila Rocca
- Max Planck Research Group and Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Lara Grysczyk
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Benedikt Martin
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Anneli Gebhardt-Wolf
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Armin Wiegering
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Markus Diefenbacher
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL/CPC-M), Munich, Germany
- Ludwig-Maximilian-Universität München (LMU), Munich, Germany
| | - Georg Gasteiger
- Max Planck Research Group and Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Dieter Saur
- Institute of Translational Cancer Research, TUM School of Medicine and Health, Munich, Germany
| | - Martin Eilers
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | | | - Florian Erhard
- Computational Systems Virology and Bioinformatics, Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Elmar Wolf
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
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Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL. Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C. eLife 2024; 13:RP94869. [PMID: 38809771 PMCID: PMC11139478 DOI: 10.7554/elife.94869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a 'pincer-like' conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
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Affiliation(s)
- Alexander S Baier
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Medical Scientist Training Program, T.H. Chan School of Medicine, University of MassachusettsBostonUnited States
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Interdisciplinary Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Priit Eek
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
- Department of Chemistry and Biotechnology, Tallinn University of TechnologyTallinnEstonia
| | - Erik M Leith
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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3
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Tian Q, Yin Y, Tian Y, Wang Y, Wang Y, Fukunaga R, Fujii T, Liao A, Li L, Zhang W, He X, Xiang W, Zhou L. Chromatin Modifier EP400 Regulates Oocyte Quality and Zygotic Genome Activation in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308018. [PMID: 38493496 PMCID: PMC11132066 DOI: 10.1002/advs.202308018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/05/2024] [Indexed: 03/19/2024]
Abstract
Epigenetic modifiers that accumulate in oocytes, play a crucial role in steering the developmental program of cleavage embryos and initiating life. However, the identification of key maternal epigenetic regulators remains elusive. In the findings, the essential role of maternal Ep400, a chaperone for H3.3, in oocyte quality and early embryo development in mice is highlighted. Depletion of Ep400 in oocytes resulted in a decline in oocyte quality and abnormalities in fertilization. Preimplantation embryos lacking maternal Ep400 exhibited reduced major zygotic genome activation (ZGA) and experienced developmental arrest at the 2-to-4-cell stage. The study shows that EP400 forms protein complex with NFYA, occupies promoters of major ZGA genes, modulates H3.3 distribution between euchromatin and heterochromatin, promotes transcription elongation, activates the expression of genes regulating mitochondrial functions, and facilitates the expression of rate-limiting enzymes of the TCA cycle. This intricate process driven by Ep400 ensures the proper execution of the developmental program, emphasizing its critical role in maternal-to-embryonic transition.
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Affiliation(s)
- Qing Tian
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Department of Gynecology and ObstetricsZhongnan Hospital of Wuhan UniversityWuhanHubei430071China
| | - Ying Yin
- Department of PhysiologySchool of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Center for Genomics and Proteomics ResearchSchool of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic EvaluationHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Yu Tian
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Yufan Wang
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Yong‐feng Wang
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Rikiro Fukunaga
- Department of BiochemistryOsaka Medical and Pharmaceutical UniversityTakatsukiOsaka569‐1094Japan
| | - Toshihiro Fujii
- Department of BiochemistryOsaka Medical and Pharmaceutical UniversityTakatsukiOsaka569‐1094Japan
| | - Ai‐hua Liao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
| | - Wei Zhang
- Department of Gynecology and ObstetricsZhongnan Hospital of Wuhan UniversityWuhanHubei430071China
| | - Ximiao He
- Department of PhysiologySchool of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Center for Genomics and Proteomics ResearchSchool of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic EvaluationHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Wenpei Xiang
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Li‐quan Zhou
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
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4
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Liu W, Liu X, Li L, Tai Z, Li G, Liu JX. EPC1/2 regulate hematopoietic stem and progenitor cell proliferation by modulating H3 acetylation and DLST. iScience 2024; 27:109263. [PMID: 38439957 PMCID: PMC10910311 DOI: 10.1016/j.isci.2024.109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/21/2023] [Accepted: 02/14/2024] [Indexed: 03/06/2024] Open
Abstract
Enhancers of polycomb 1 (EPC1) and 2 (EPC2) are involved in multiple biological processes as components of histone acetyltransferases/deacetylase complexes and transcriptional cofactors, and their dysfunction was associated with developmental defects and diseases. However, it remains unknown how their dysfunction induces hematopoietic stem and progenitor cell (HSPC) defects. Here, we show that depletion of EPC1/2 significantly reduced the number of hematopoietic stem and progenitor cells (HSPCs) in the aorta-gonad mesonephros and caudal hematopoietic tissue regions by impairing HSPC proliferation, and consistently downregulated the expression of HSPC genes in K562 cells. This study demonstrates the functions of EPC1/2 in regulating histone H3 acetylation, and in regulating DLST (dihydrolipoamide S-succinyltransferase) via H3 acetylation and cooperating with transcription factors serum response factor and FOXR2 together, and in the subsequent HSPC emergence and proliferation. Our results demonstrate the essential roles of EPC1/2 in regulating H3 acetylation, and DLST as a linkage between EPC1 and EPC2 with mitochondria metabolism, in HSPC emergence and proliferation.
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Affiliation(s)
- WenYe Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - LingYa Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - ZhiPeng Tai
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - GuoLiang Li
- College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing-Xia Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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5
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Ferrer P, Upadhyay S, Cai JJ, Clement TM. Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582797. [PMID: 38464253 PMCID: PMC10925299 DOI: 10.1101/2024.02.29.582797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
A mechanistic role for nuclear function of testis-specific actin related proteins (ARPs) is proposed here through contributions of ARP subunit swapping in canonical chromatin regulatory complexes. This is significant to our understanding of both mechanisms controlling regulation of spermiogenesis, and the expanding functional roles of the ARPs in cell biology. Among these roles, actins and ARPs are pivotal not only in cytoskeletal regulation, but also in intranuclear chromatin organization, influencing gene regulation and nucleosome remodeling. This study focuses on two testis-specific ARPs, ACTL7A and ACTL7B, exploring their intranuclear activities and broader implications utilizing combined in vivo, in vitro, and in silico approaches. ACTL7A and ACTL7B, previously associated with structural roles, are hypothesized here to serve in chromatin regulation during germline development. This study confirms the intranuclear presence of ACTL7B in spermatocytes and round spermatids, revealing a potential role in intranuclear processes, and identifies a putative nuclear localization sequence conserved across mammalian ACTL7B, indicating a potentially unique mode of nuclear transport which differs from conventional actin. Ablation of ACTL7B leads to varied transcriptional changes reported here. Additionally, in the absence of ACTL7A or ACTL7B there is a loss of intranuclear localization of HDAC1 and HDAC3, which are known regulators of epigenetic associated acetylation changes that in turn regulate gene expression. Thus, these HDACs are implicated as contributors to the aberrant gene expression observed in the KO mouse testis transcriptomic analysis. Furthermore, this study employed and confirmed the accuracy of in silico models to predict ARP interactions with Helicase-SANT-associated (HSA) domains, uncovering putative roles for testis-specific ARPs in nucleosome remodeling complexes. In these models, ACTL7A and ACTL7B were found capable of binding to INO80 and SWI/SNF nucleosome remodeler family members in a manner akin to nuclear actin and ACTL6A. These models thus implicate germline-specific ARP subunit swapping within chromatin regulatory complexes as a potential regulatory mechanism for chromatin and associated molecular machinery adaptations in nuclear reorganizations required during spermiogenesis. These results hold implications for male fertility and epigenetic programing in the male-germline that warrant significant future investigation. In summary, this study reveals that ACTL7A and ACTL7B play intranuclear gene regulation roles in male gametogenesis, adding to the multifaceted roles identified also spanning structural, acrosomal, and flagellar stability. ACTL7A and ACTL7B unique nuclear transport, impact on HDAC nuclear associations, impact on transcriptional processes, and proposed mechanism for involvement in nucleosome remodeling complexes supported by AI facilitated in silico modeling contribute to a more comprehensive understanding of the indispensable functions of ARPs broadly in cell biology, and specifically in male fertility.
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Affiliation(s)
- Pierre Ferrer
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - James J Cai
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Tracy M Clement
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
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Zemke NR, Hsu E, Barshop WD, Sha J, Wohlschlegel JA, Berk AJ. Adenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stress. J Virol 2023; 97:e0099323. [PMID: 37962355 PMCID: PMC10734532 DOI: 10.1128/jvi.00993-23] [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: 07/08/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Inactivation of EP300/CREBB paralogous cellular lysine acetyltransferases (KATs) during the early phase of infection is a consistent feature of DNA viruses. The cell responds by stabilizing transcription factor IRF3 which activates transcription of scores of interferon-stimulated genes (ISGs), inhibiting viral replication. Human respiratory adenoviruses counter this by assembling a CUL4-based ubiquitin ligase complex that polyubiquitinylates RUVBL1 and 2 inducing their proteasomal degradation. This inhibits accumulation of active IRF3 and the expression of anti-viral ISGs, allowing replication of the respiratory HAdVs in the face of inhibition of EP300/CBEBBP KAT activity by the N-terminal region of E1A.
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Affiliation(s)
- Nathan R. Zemke
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Emily Hsu
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - William D. Barshop
- Thermo Fisher Scientific, San Jose, California, USA
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, California, USA
| | - Jihui Sha
- Thermo Fisher Scientific, San Jose, California, USA
| | - James A. Wohlschlegel
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Thermo Fisher Scientific, San Jose, California, USA
| | - Arnold J. Berk
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
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7
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Wang Z, Cai H, Li Z, Sun W, Zhao E, Cui H. Histone demethylase KDM4B accelerates the progression of glioblastoma via the epigenetic regulation of MYC stability. Clin Epigenetics 2023; 15:192. [PMID: 38093312 PMCID: PMC10720090 DOI: 10.1186/s13148-023-01608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most malignant and invasive human brain tumor. Histone demethylase 4B (KDM4B) is abnormally expressed in GBM, but the molecular mechanisms by which KDM4B affects the malignant tumor progression are not well defined. METHODS GBM cell lines and xenograft tumor samples were subjected to quantitative PCR (qPCR), Western blot, immunohistochemical staining (IHC), as well as ubiquitination, immunoprecipitation (IP), and chromatin immunoprecipitation (ChIP) assays to investigate the role of KDM4B in the progression of GBM. RESULTS Here, we report that KDM4B is an epigenetic activator of GBM progression. Abnormal expression of KDM4B is correlated with a poor prognosis in GBM patients. In GBM cell lines, KDM4B silencing significantly inhibited cell survival, proliferation, migration, and invasion, indicating that KDM4B is essential for the anchorage-independent growth and tumorigenic activity of GBM cells. Mechanistically, KDM4B silencing led to downregulation of the oncoprotein MYC and suppressed the expression of cell cycle proteins and epithelial-to-mesenchymal transition (EMT)-related proteins. Furthermore, we found that KDM4B regulates MYC stability through the E3 ligase complex SCFFBXL3+CRY2 and epigenetically activates the transcription of CCNB1 by removing the repressive chromatin mark histone H3 lysine 9 trimethylation (H3K9me3). Finally, we provide evidence that KDM4B epigenetically activates the transcription of miR-181d-5p, which enhances MYC stability. CONCLUSIONS Our study has uncovered a KDM4B-dependent epigenetic mechanism in the control of tumor progression, providing a rationale for utilizing KDM4B as a promising therapeutic target for the treatment of MYC-amplified GBM.
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Affiliation(s)
- Zhongze Wang
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Huarui Cai
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
| | - Zekun Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
| | - Wei Sun
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
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8
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Fasano C, Lepore Signorile M, Di Nicola E, Pantaleo A, Forte G, De Marco K, Sanese P, Disciglio V, Grossi V, Simone C. The chromatin remodeling factors EP300 and TRRAP are novel SMYD3 interactors involved in the emerging 'nonmutational epigenetic reprogramming' cancer hallmark. Comput Struct Biotechnol J 2023; 21:5240-5248. [PMID: 37954147 PMCID: PMC10632561 DOI: 10.1016/j.csbj.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023] Open
Abstract
SMDY3 is a histone-lysine N-methyltransferase involved in several oncogenic processes and is believed to play a major role in various cancer hallmarks. Recently, we identified ATM, BRCA2, CHK2, MTOR, BLM, MET, AMPK, and p130 as direct SMYD3 interactors by taking advantage of a library of rare tripeptides, which we first tested for their in vitro binding affinity to SMYD3 and then used as in silico probes to systematically search the human proteome. Here, we used this innovative approach to identify further SMYD3-interacting proteins involved in crucial cancer pathways and found that the chromatin remodeling factors EP300 and TRRAP interact directly with SMYD3, thus linking SMYD3 to the emerging 'nonmutational epigenetic reprogramming' cancer hallmark. Of note, we validated these interactions in gastrointestinal cancer cell lines, including HCT-116 cells, which harbor a C-terminal truncating mutation in EP300, suggesting that EP300 binds to SMYD3 via its N-terminal region. While additional studies are required to ascertain the functional mechanisms underlying these interactions and their significance, the identification of two novel SMYD3 interactors involved in epigenetic cancer hallmark pathways adds important pieces to the puzzle of how SMYD3 exerts its oncogenic role.
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Affiliation(s)
- Candida Fasano
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Elisabetta Di Nicola
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology - IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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9
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Li Z, Kim H, Kim J, Park JH. EP400NL is involved in PD-L1 gene activation by forming a transcriptional coactivator complex. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194889. [PMID: 36328277 DOI: 10.1016/j.bbagrm.2022.194889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022]
Abstract
EP400 is an ATP-dependent chromatin remodelling enzyme that regulates DNA double-strand break repair and transcription, including cMyc-dependent gene expression. We previously showed that the N-terminal domain of EP400 increases the efficacy of chemotherapeutic drugs against cancer cells. As the EP400 N-terminal-Like (EP400NL) gene resides next to the EP400 gene locus, this prompted us to investigate whether EP400NL plays a similar role in transcriptional regulation to the full-length EP400 protein. We found that EP400NL forms a human NuA4-like chromatin remodelling complex that lacks both the TIP60 histone acetyltransferase and EP400 ATPase. However, this EP400NL complex displays H2A.Z deposition activity on a chromatin template comparable to the human NuA4 complex, suggesting another associated ATPase such as BRG1 or RuvBL1/RuvBL2 catalyses the reaction. We demonstrated that the transcriptional coactivator function of EP400NL is required for serum and IFNγ-induced PD-L1 gene activation. Furthermore, transcriptome analysis indicates that EP400NL contributes to cMyc-responsive mitochondrial biogenesis. Taken together, our studies show that EP400NL plays a role as a transcription coactivator of PD-L1 gene regulation and provides a potential target to modulate cMyc functions in cancer therapy.
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Affiliation(s)
- Zidong Li
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Hyoungmin Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
| | - Jeong Hyeon Park
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
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10
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Akcan TS, Vilov S, Heinig M. Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures. Nucleic Acids Res 2023; 51:1608-1624. [PMID: 36727445 PMCID: PMC9976927 DOI: 10.1093/nar/gkac1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
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Affiliation(s)
- Toray S Akcan
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany
| | - Sergey Vilov
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
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11
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Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. Int J Mol Sci 2023; 24:1051. [PMID: 36674565 PMCID: PMC9864664 DOI: 10.3390/ijms24021051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Ellyn Rousselot
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Stéphane Téletchéa
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Céline Noirot
- INRAE, UR 875 Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo Auzeville, 31326 Castanet-Tolosan, France
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Josien van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Christophe Thiriet
- Université Rennes 1, CNRS, IGDR (Institut de Génétique et Développement de Rennes)—UMR 6290, 35043 Rennes, France
| | - Céline Duc
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
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12
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Rapchak K, Yagobian SD, Moore J, Khattri M, Shuda M. Merkel cell polyomavirus small T antigen is a viral transcription activator that is essential for viral genome maintenance. PLoS Pathog 2022; 18:e1011039. [PMID: 36574443 PMCID: PMC9829177 DOI: 10.1371/journal.ppat.1011039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/09/2023] [Accepted: 12/01/2022] [Indexed: 12/29/2022] Open
Abstract
Merkel cell polyomavirus (MCV) is a small DNA tumor virus that persists in human skin and causes Merkel cell carcinoma (MCC) in immunocompromised individuals. The multi-functional protein MCV small T (sT) activates viral DNA replication by stabilizing large T (LT) and promotes cell transformation through the LT stabilization domain (LTSD). Using MCVΔsT, a mutant MCV clone that ablates sT, we investigated the role of sT in MCV genome maintenance. sT was dispensable for initiation of viral DNA replication, but essential for maintenance of the MCV genome and activation of viral early and late gene expression for progression of the viral lifecycle. Furthermore, in phenotype rescue studies, exogenous sT activated viral DNA replication and mRNA expression in MCVΔsT through the LTSD. While exogenous LT expression, which mimics LT stabilization, increased viral DNA replication, it did not activate viral mRNA expression. After cataloging transcriptional regulator proteins by proximity-based MCV sT-host protein interaction analysis, we validated LTSD-dependent sT interaction with four transcriptional regulators: Cux1, c-Jun, BRD9, and CBP. Functional studies revealed Cux1 and c-Jun as negative regulators, and CBP and BRD9 as positive regulators of MCV transcription. CBP inhibitor A-485 suppressed sT-induced viral gene activation in replicating MCVΔsT and inhibited early gene expression in MCV-integrated MCC cells. These results suggest that sT promotes viral lifecycle progression by activating mRNA expression and capsid protein production through interaction with the transcriptional regulators. This activity is essential for MCV genome maintenance, suggesting a critical role of sT in MCV persistence and MCC carcinogenesis.
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Affiliation(s)
- Kyle Rapchak
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Shiva D. Yagobian
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Jackson Moore
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Michelle Khattri
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Masahiro Shuda
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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13
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MYC multimers shield stalled replication forks from RNA polymerase. Nature 2022; 612:148-155. [PMID: 36424410 DOI: 10.1038/s41586-022-05469-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022]
Abstract
Oncoproteins of the MYC family drive the development of numerous human tumours1. In unperturbed cells, MYC proteins bind to nearly all active promoters and control transcription by RNA polymerase II2,3. MYC proteins can also coordinate transcription with DNA replication4,5 and promote the repair of transcription-associated DNA damage6, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from many of its binding sites in active promoters and forms multimeric, often sphere-like structures in response to perturbation of transcription elongation, mRNA splicing or inhibition of the proteasome. Multimerization is accompanied by a global change in the MYC interactome towards proteins involved in transcription termination and RNA processing. MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround FANCD2, ATR and BRCA1 proteins, which are located at stalled forks7,8. MYC multimerization is triggered in a HUWE16 and ubiquitylation-dependent manner. At active promoters, MYC multimers block antisense transcription and stabilize FANCD2 association with chromatin. This limits DNA double strand break formation during S-phase, suggesting that the multimerization of MYC enables tumour cells to proliferate under stressful conditions.
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14
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Fusi L, Paudel R, Meder K, Schlosser A, Schrama D, Goebeler M, Schmidt M. Interaction of transcription factor FoxO3 with histone acetyltransferase complex subunit TRRAP Modulates Gene Expression and Apoptosis. J Biol Chem 2022; 298:101714. [PMID: 35151693 PMCID: PMC8914384 DOI: 10.1016/j.jbc.2022.101714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/28/2021] [Accepted: 01/19/2022] [Indexed: 11/01/2022] Open
Abstract
Forkhead box O (FoxO) transcription factors are conserved proteins involved in the regulation of life span and age-related diseases, such as diabetes and cancer. Stress stimuli or growth factor deprivation promotes nuclear localization and activation of FoxO proteins, which—depending on the cellular context—can lead to cell cycle arrest or apoptosis. In endothelial cells (ECs), they further regulate angiogenesis and may promote inflammation and vessel destabilization implicating a role of FoxOs in vascular diseases. In several cancers, FoxOs exert a tumor-suppressive function by regulating proliferation and survival. We and others have previously shown that FoxOs can regulate these processes via two different mechanisms: by direct binding to forkhead-responsive elements at the promoter of target genes or by a poorly understood alternative process that does not require direct DNA binding and regulates key targets in primary human ECs. Here, we performed an interaction study in ECs to identify new nuclear FoxO3 interaction partners that might contribute to FoxO-dependent gene regulation. Mass spectrometry analysis of FoxO3-interacting proteins revealed transformation/transcription domain–associated protein (TRRAP), a member of multiple histone acetyltransferase complexes, as a novel binding partner of FoxO family proteins. We demonstrate that TRRAP is required to support FoxO3 transactivation and FoxO3-dependent G1 arrest and apoptosis in ECs via transcriptional activation of the cyclin-dependent kinase inhibitor p27kip1 and the proapoptotic B-cell lymphoma 2 family member, BIM. Moreover, FoxO–TRRAP interaction could explain FoxO-induced alternative gene regulation via TRRAP-dependent recruitment to target promoters lacking forkhead-responsive element sequences.
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15
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Tessier TM, Dodge MJ, MacNeil KM, Evans AM, Prusinkiewicz MA, Mymryk JS. Almost famous: Human adenoviruses (and what they have taught us about cancer). Tumour Virus Res 2021; 12:200225. [PMID: 34500123 PMCID: PMC8449131 DOI: 10.1016/j.tvr.2021.200225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 12/11/2022] Open
Abstract
Papillomaviruses, polyomaviruses and adenoviruses are collectively categorized as the small DNA tumour viruses. Notably, human adenoviruses were the first human viruses demonstrated to be able to cause cancer, albeit in non-human animal models. Despite their long history, no human adenovirus is a known causative agent of human cancers, unlike a subset of their more famous cousins, including human papillomaviruses and human Merkel cell polyomavirus. Nevertheless, seminal research using human adenoviruses has been highly informative in understanding the basics of cell cycle control, gene expression, apoptosis and cell differentiation. This review highlights the contributions of human adenovirus research in advancing our knowledge of the molecular basis of cancer.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Andris M Evans
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Martin A Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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16
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Mödlhammer A, Pfurtscheller S, Feichtner A, Hartl M, Schneider R. The Diarylheptanoid Curcumin Induces MYC Inhibition and Cross-Links This Oncoprotein to the Coactivator TRRAP. Front Oncol 2021; 11:660481. [PMID: 33937075 PMCID: PMC8082493 DOI: 10.3389/fonc.2021.660481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
The c-Myc protein (MYC) is a transcription factor with strong oncogenic potential controlling fundamental cellular processes. In most human tumors, MYC is overexpressed by enhanced transcriptional activation, gene amplification, chromosomal rearrangements, or increased protein stabilization. To pharmacologically suppress oncogenic MYC functions, multiple approaches have been applied either to inhibit transcriptional activation of the endogenous MYC gene, or to interfere with biochemical functions of aberrantly activated MYC. Other critical points of attack are targeted protein modification, or destabilization leading to a non-functional MYC oncoprotein. It has been claimed that the natural compound curcumin representing the principal curcumoid of turmeric (Curcuma longa) has anticancer properties although its specificity, efficacy, and the underlying molecular mechanisms have been controversially discussed. Here, we have tested curcumin’s effect on MYC-dependent cell transformation and transcriptional activation, and found that this natural compound interferes with both of these MYC activities. Furthermore, in curcumin-treated cells, the endogenous 60-kDa MYC protein is covalently and specifically cross-linked to one of its transcriptional interaction partners, namely the 434-kDa transformation/transcription domain associated protein (TRRAP). Thereby, endogenous MYC levels are strongly reduced and cells stop to proliferate. TRRAP is a multidomain adaptor protein of the phosphoinositide 3-kinase-related kinases (PIKK) family and represents an important component of many histone acetyltransferase (HAT) complexes. TRRAP is important to mediate transcriptional activation executed by the MYC oncoprotein, but on the other hand TRRAP also negatively regulates protein stability of the tumor suppressor p53 (TP53). Curcumin-mediated covalent binding of MYC to TRRAP reduces the protein amounts of both interaction partners but does not downregulate TP53, so that the growth-arresting effect of wild type TP53 could prevail. Our results elucidate a molecular mechanism of curcumin action that specifically and irreversibly targets two crucial multifunctional cellular players. With regard to their broad impact in cancer, our findings contribute to explain the pleiotropic functions of curcumin, and suggest that this natural spice, or more bioavailable derivatives thereof, may constitute useful adjuvants in the therapy of MYC-dependent and TRRAP-associated human tumors.
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Affiliation(s)
- Alexander Mödlhammer
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Sandra Pfurtscheller
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Rainer Schneider
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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17
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Gene Transactivation and Transrepression in MYC-Driven Cancers. Int J Mol Sci 2021; 22:ijms22073458. [PMID: 33801599 PMCID: PMC8037706 DOI: 10.3390/ijms22073458] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
MYC is a proto-oncogene regulating a large number of genes involved in a plethora of cellular functions. Its deregulation results in activation of MYC gene expression and/or an increase in MYC protein stability. MYC overexpression is a hallmark of malignant growth, inducing self-renewal of stem cells and blocking senescence and cell differentiation. This review summarizes the latest advances in our understanding of MYC-mediated molecular mechanisms responsible for its oncogenic activity. Several recent findings indicate that MYC is a regulator of cancer genome and epigenome: MYC modulates expression of target genes in a site-specific manner, by recruiting chromatin remodeling co-factors at promoter regions, and at genome-wide level, by regulating the expression of several epigenetic modifiers that alter the entire chromatin structure. We also discuss novel emerging therapeutic strategies based on both direct modulation of MYC and its epigenetic cofactors.
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18
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Liu R, Shi P, Wang Z, Yuan C, Cui H. Molecular Mechanisms of MYCN Dysregulation in Cancers. Front Oncol 2021; 10:625332. [PMID: 33614505 PMCID: PMC7886978 DOI: 10.3389/fonc.2020.625332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
MYCN, a member of MYC proto-oncogene family, encodes a basic helix-loop-helix transcription factor N-MYC. Abnormal expression of N-MYC is correlated with high-risk cancers and poor prognosis. Initially identified as an amplified oncogene in neuroblastoma in 1983, the oncogenic effect of N-MYC is expanded to multiple neuronal and nonneuronal tumors. Direct targeting N-MYC remains challenge due to its "undruggable" features. Therefore, alternative therapeutic approaches for targeting MYCN-driven tumors have been focused on the disruption of transcription, translation, protein stability as well as synthetic lethality of MYCN. In this review, we summarize the latest advances in understanding the molecular mechanisms of MYCN dysregulation in cancers.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Pengfei Shi
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaoyu Yuan
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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19
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Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol Cell 2021; 81:830-844.e13. [PMID: 33453168 DOI: 10.1016/j.molcel.2020.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
The MYC oncoprotein globally affects the function of RNA polymerase II (RNAPII). The ability of MYC to promote transcription elongation depends on its ubiquitylation. Here, we show that MYC and PAF1c (polymerase II-associated factor 1 complex) interact directly and mutually enhance each other's association with active promoters. PAF1c is rapidly transferred from MYC onto RNAPII. This transfer is driven by the HUWE1 ubiquitin ligase and is required for MYC-dependent transcription elongation. MYC and HUWE1 promote histone H2B ubiquitylation, which alters chromatin structure both for transcription elongation and double-strand break repair. Consistently, MYC suppresses double-strand break accumulation in active genes in a strictly PAF1c-dependent manner. Depletion of PAF1c causes transcription-dependent accumulation of double-strand breaks, despite widespread repair-associated DNA synthesis. Our data show that the transfer of PAF1c from MYC onto RNAPII efficiently couples transcription elongation with double-strand break repair to maintain the genomic integrity of MYC-driven tumor cells.
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20
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Arede L, Pina C. Buffering noise: KAT2A modular contributions to stabilization of transcription and cell identity in cancer and development. Exp Hematol 2020; 93:25-37. [PMID: 33223444 DOI: 10.1016/j.exphem.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
KAT2A is a histone acetyltransferase recently identified as a vulnerability in at least some forms of Acute Myeloid Leukemia (AML). Its loss or inhibition prompts leukemia stem cells out of self-renewal and into differentiation with ultimate exhaustion of the leukemia pool. We have recently linked the Kat2a requirement in AML to control of transcriptional noise, reflecting an evolutionary-conserved role of Kat2a in promoting burst-like promoter activity and stabilizing gene expression. We suggest that through this role, Kat2a contributes to preservation of cell identity. KAT2A exerts its acetyltransferase activity in the context of two macromolecular complexes, Spt-Ada-Gcn5-Acetyltransferase (SAGA) and Ada-Two-A-Containing (ATAC), but the specific contribution of each complex to stabilization of gene expression is currently unknown. By reviewing specific gene targets and requirements of the two complexes in cancer and development, we suggest that SAGA regulates lineage-specific programs, and ATAC maintains biosynthetic activity through control of ribosomal protein and translation-associated genes, on which cells may be differentially dependent. While our data suggest that KAT2A-mediated regulation of transcriptional noise in AML may be exerted through ATAC, we discuss potential caveats and probe general vs. complex-specific contributions of KAT2A to transcriptional stability, with implications for control and perturbation of cell identity.
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Affiliation(s)
- Liliana Arede
- Departments of Haematology; Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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21
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Saha B, Parks RJ. Recent Advances in Novel Antiviral Therapies against Human Adenovirus. Microorganisms 2020; 8:microorganisms8091284. [PMID: 32842697 PMCID: PMC7563841 DOI: 10.3390/microorganisms8091284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Human adenovirus (HAdV) is a very common pathogen that typically causes minor disease in most patients. However, the virus can cause significant morbidity and mortality in certain populations, including young children, the elderly, and those with compromised immune systems. Currently, there are no approved therapeutics to treat HAdV infections, and the standard treatment relies on drugs approved to combat other viral infections. Such treatments often show inconsistent efficacy, and therefore, more effective antiviral therapies are necessary. In this review, we discuss recent developments in the search for new chemical and biological anti-HAdV therapeutics, including drugs that are currently undergoing preclinical/clinical testing, and small molecule screens for the identification of novel compounds that abrogate HAdV replication and disease.
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Affiliation(s)
- Bratati Saha
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Robin J. Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada
- Correspondence: ; Tel.: +1-613-737-8123
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22
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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23
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Ip WH, Dobner T. Cell transformation by the adenovirus oncogenes E1 and E4. FEBS Lett 2019; 594:1848-1860. [PMID: 31821536 DOI: 10.1002/1873-3468.13717] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022]
Abstract
Extensive studies on viral-mediated oncogenic transformation by human adenoviruses have revealed much of our current understanding on the molecular mechanisms that are involved in the process. To date, these studies have shown that cell transformation is a multistep process regulated by the cooperation of several adenoviral gene products encoded in the early regions 1 (E1) and 4 (E4). Early region 1A immortalizes primary rodent cells, whereas co-expression of early region protein 1B induces full manifestation of the transformed phenotype. Beside E1 proteins, also some E4 proteins have partial transforming activities through regulating many cellular pathways. Here, we summarize recent data of how adenoviral oncoproteins may contribute to viral transformation and discuss the challenge of pinpointing the underlying mechanisms.
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Affiliation(s)
- Wing Hang Ip
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Thomas Dobner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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24
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El Hadidy N, Uversky VN. Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development. Int J Mol Sci 2019; 20:ijms20215260. [PMID: 31652801 PMCID: PMC6862534 DOI: 10.3390/ijms20215260] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
The two-meter-long DNA is compressed into chromatin in the nucleus of every cell, which serves as a significant barrier to transcription. Therefore, for processes such as replication and transcription to occur, the highly compacted chromatin must be relaxed, and the processes required for chromatin reorganization for the aim of replication or transcription are controlled by ATP-dependent nucleosome remodelers. One of the most highly studied remodelers of this kind is the BRG1- or BRM-associated factor complex (BAF complex, also known as SWItch/sucrose non-fermentable (SWI/SNF) complex), which is crucial for the regulation of gene expression and differentiation in eukaryotes. Chromatin remodeling complex BAF is characterized by a highly polymorphic structure, containing from four to 17 subunits encoded by 29 genes. The aim of this paper is to provide an overview of the role of BAF complex in chromatin remodeling and also to use literature mining and a set of computational and bioinformatics tools to analyze structural properties, intrinsic disorder predisposition, and functionalities of its subunits, along with the description of the relations of different BAF complex subunits to the pathogenesis of various human diseases.
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Affiliation(s)
- Nashwa El Hadidy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290 Moscow Region, Russia.
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25
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Giaimo BD, Ferrante F, Vallejo DM, Hein K, Gutierrez-Perez I, Nist A, Stiewe T, Mittler G, Herold S, Zimmermann T, Bartkuhn M, Schwarz P, Oswald F, Dominguez M, Borggrefe T. Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response. Nucleic Acids Res 2019; 46:8197-8215. [PMID: 29986055 PMCID: PMC6144792 DOI: 10.1093/nar/gky551] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/28/2018] [Indexed: 02/04/2023] Open
Abstract
A fundamental as yet incompletely understood feature of Notch signal transduction is a transcriptional shift from repression to activation that depends on chromatin regulation mediated by transcription factor RBP-J and associated cofactors. Incorporation of histone variants alter the functional properties of chromatin and are implicated in the regulation of gene expression. Here, we show that depletion of histone variant H2A.Z leads to upregulation of canonical Notch target genes and that the H2A.Z-chaperone TRRAP/p400/Tip60 complex physically associates with RBP-J at Notch-dependent enhancers. When targeted to RBP-J-bound enhancers, the acetyltransferase Tip60 acetylates H2A.Z and upregulates Notch target gene expression. Importantly, the Drosophila homologs of Tip60, p400 and H2A.Z modulate Notch signaling response and growth in vivo. Together, our data reveal that loading and acetylation of H2A.Z are required to assure tight control of canonical Notch activation.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albertstrasse 19A, 79104 Freiburg, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Diana M Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Irene Gutierrez-Perez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Universities Giessen & Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Peggy Schwarz
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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26
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Klages-Mundt NL, Kumar A, Zhang Y, Kapoor P, Shen X. The Nature of Actin-Family Proteins in Chromatin-Modifying Complexes. Front Genet 2018; 9:398. [PMID: 30319687 PMCID: PMC6167448 DOI: 10.3389/fgene.2018.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/31/2018] [Indexed: 01/25/2023] Open
Abstract
Actin is not only one of the most abundant proteins in eukaryotic cells, but also one of the most versatile. In addition to its familiar involvement in enabling contraction and establishing cellular motility and scaffolding in the cytosol, actin has well-documented roles in a variety of processes within the confines of the nucleus, such as transcriptional regulation and DNA repair. Interestingly, monomeric actin as well as actin-related proteins (Arps) are found as stoichiometric subunits of a variety of chromatin remodeling complexes and histone acetyltransferases, raising the question of precisely what roles they serve in these contexts. Actin and Arps are present in unique combinations in chromatin modifiers, helping to establish structural integrity of the complex and enabling a wide range of functions, such as recruiting the complex to nucleosomes to facilitate chromatin remodeling and promoting ATPase activity of the catalytic subunit. Actin and Arps are also thought to help modulate chromatin dynamics and maintain higher-order chromatin structure. Moreover, the presence of actin and Arps in several chromatin modifiers is necessary for promoting genomic integrity and an effective DNA damage response. In this review, we discuss the involvement of actin and Arps in these nuclear complexes that control chromatin remodeling and histone modifications, while also considering avenues for future study to further shed light on their functional importance.
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Affiliation(s)
- Naeh L Klages-Mundt
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Yuexuan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Xuetong Shen
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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27
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Idrissou M, Rifaï K, Daures M, Penault-Llorca F, Bignon YJ, Bernard-Gallon D. Exciting History of Tip60 and Its Companions in Carcinogenesis Across the Heterochromatin Landscapes. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:626-628. [PMID: 30106669 DOI: 10.1089/omi.2018.0122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Mouhamed Idrissou
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,2 INSERM U 1240-IMOST , Clermont-Ferrand, France
| | - Khaldoun Rifaï
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,2 INSERM U 1240-IMOST , Clermont-Ferrand, France
| | - Marine Daures
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,2 INSERM U 1240-IMOST , Clermont-Ferrand, France
| | - Frédérique Penault-Llorca
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,3 Department of Biopathology, Centre Jean Perrin , Clermont-Ferrand, France
| | - Yves-Jean Bignon
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,2 INSERM U 1240-IMOST , Clermont-Ferrand, France
| | - Dominique Bernard-Gallon
- 1 Department of Oncogenetics, Centre Jean Perrin , CBRV, Clermont-Ferrand, France .,2 INSERM U 1240-IMOST , Clermont-Ferrand, France
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28
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Rust K, Tiwari MD, Mishra VK, Grawe F, Wodarz A. Myc and the Tip60 chromatin remodeling complex control neuroblast maintenance and polarity in Drosophila. EMBO J 2018; 37:embj.201798659. [PMID: 29997178 DOI: 10.15252/embj.201798659] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 02/04/2023] Open
Abstract
Stem cells establish cortical polarity and divide asymmetrically to simultaneously maintain themselves and generate differentiating offspring cells. Several chromatin modifiers have been identified as stemness factors in mammalian pluripotent stem cells, but whether these factors control stem cell polarity and asymmetric division has not been investigated so far. We addressed this question in Drosophila neural stem cells called neuroblasts. We identified the Tip60 chromatin remodeling complex and its interaction partner Myc as regulators of genes required for neuroblast maintenance. Knockdown of Tip60 complex members results in loss of cortical polarity, symmetric neuroblast division, and premature differentiation through nuclear entry of the transcription factor Prospero. We found that aPKC is the key target gene of Myc and the Tip60 complex subunit Domino in regulating neuroblast polarity. Our transcriptome analysis further showed that Domino regulates the expression of mitotic spindle genes previously identified as direct Myc targets. Our findings reveal an evolutionarily conserved functional link between Myc, the Tip60 complex, and the molecular network controlling cell polarity and asymmetric cell division.
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Affiliation(s)
- Katja Rust
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne, Germany .,Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne, Germany.,Stem Cell Biology, Institute for Anatomy and Cell Biology, Georg-August University Göttingen, Göttingen, Germany.,Department of Anatomy and OB-GYN/RS, University of California, San Francisco, San Francisco, CA, USA
| | - Manu D Tiwari
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne, Germany.,Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne, Germany.,Stem Cell Biology, Institute for Anatomy and Cell Biology, Georg-August University Göttingen, Göttingen, Germany
| | - Vivek Kumar Mishra
- Department of Dermatology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ferdi Grawe
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne, Germany
| | - Andreas Wodarz
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne, Germany .,Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne, Germany.,Stem Cell Biology, Institute for Anatomy and Cell Biology, Georg-August University Göttingen, Göttingen, Germany
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29
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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.
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30
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Büchel G, Carstensen A, Mak KY, Roeschert I, Leen E, Sumara O, Hofstetter J, Herold S, Kalb J, Baluapuri A, Poon E, Kwok C, Chesler L, Maric HM, Rickman DS, Wolf E, Bayliss R, Walz S, Eilers M. Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle. Cell Rep 2017; 21:3483-3497. [PMID: 29262328 PMCID: PMC5746598 DOI: 10.1016/j.celrep.2017.11.090] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/12/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (Pol II). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A, and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of Pol II promoters and intergenic regions. TFIIIC promotes association of RAD21 with N-MYC target sites and is required for N-MYC-dependent promoter escape and pause release of Pol II. Aurora-A competes with binding of TFIIIC and RAD21 to N-MYC in vitro and antagonizes association of TOP2A, TFIIIC, and RAD21 with N-MYC during S phase, blocking N-MYC-dependent release of Pol II from the promoter. Inhibition of Aurora-A in S phase restores RAD21 and TFIIIC binding to chromatin and partially restores N-MYC-dependent transcriptional elongation. We propose that complex formation with Aurora-A controls N-MYC function during the cell cycle.
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Affiliation(s)
- Gabriele Büchel
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anne Carstensen
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ka-Yan Mak
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Isabelle Roeschert
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eoin Leen
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Olga Sumara
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jacqueline Kalb
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Evon Poon
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Colin Kwok
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Louis Chesler
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Hans Michael Maric
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - David S Rickman
- Weill Cornell Medicine, Sandra and Edward Meyer Cancer Center, 413 E. 69(th) Street, New York, NY 10021, USA
| | - Elmar Wolf
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Richard Bayliss
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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31
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Zhao LJ, Loewenstein PM, Green M. Adenovirus E1A TRRAP-targeting domain-mediated enhancement of MYC association with the NuA4 complex activates a panel of MYC target genes enriched for gene expression and ribosome biogenesis. Virology 2017; 512:172-179. [PMID: 28965007 PMCID: PMC5790114 DOI: 10.1016/j.virol.2017.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 11/21/2022]
Abstract
Cellular transformation by adenovirus E1A requires targeting TRRAP, a scaffold protein which helps assemble histone acetyltransferase complexes, including the NuA4 complex. We recently reported that E1A and E1A 1-80 (N-terminal 80 aa) promote association of the proto-oncogene product MYC with the NuA4 complex. The E1A N-terminal TRRAP-targeting (ET) domain is required for E1A 1-80 to interact with the NuA4 complex. We demonstrate that an ET-MYC fusion associates with the NuA4 complex more efficiently than does MYC alone. Because MYC regulates genes for multiple cellular pathways, we performed global RNA-sequence analysis of cells expressing MYC or ET-MYC, and identified a panel of genes (262) preferentially activated by ET-MYC and significantly enriched in genes involved in gene expression and ribosome biogenesis, suggesting that E1A enhances MYC association with the NuA4 complex to activate a set of MYC target genes likely involved in cellular proliferation and cellular transformation by E1A and by MYC.
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Affiliation(s)
- Ling-Jun Zhao
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, Rm 633, 1205 Carr Lane, St. Louis, MO 63104, USA.
| | - Paul M Loewenstein
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, Rm 633, 1205 Carr Lane, St. Louis, MO 63104, USA
| | - Maurice Green
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, Rm 633, 1205 Carr Lane, St. Louis, MO 63104, USA.
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32
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Cheng J, Park DE, Berrios C, White EA, Arora R, Yoon R, Branigan T, Xiao T, Westerling T, Federation A, Zeid R, Strober B, Swanson SK, Florens L, Bradner JE, Brown M, Howley PM, Padi M, Washburn MP, DeCaprio JA. Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis. PLoS Pathog 2017; 13:e1006668. [PMID: 29028833 PMCID: PMC5640240 DOI: 10.1371/journal.ppat.1006668] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022] Open
Abstract
Merkel cell carcinoma (MCC) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). While LT binds RB and inactivates its tumor suppressor function, it is less clear how ST contributes to MCC tumorigenesis. Here we show that ST binds specifically to the MYC homolog MYCL (L-MYC) and recruits it to the 15-component EP400 histone acetyltransferase and chromatin remodeling complex. We performed a large-scale immunoprecipitation for ST and identified co-precipitating proteins by mass spectrometry. In addition to protein phosphatase 2A (PP2A) subunits, we identified MYCL and its heterodimeric partner MAX plus the EP400 complex. Immunoprecipitation for MAX and EP400 complex components confirmed their association with ST. We determined that the ST-MYCL-EP400 complex binds together to specific gene promoters and activates their expression by integrating chromatin immunoprecipitation with sequencing (ChIP-seq) and RNA-seq. MYCL and EP400 were required for maintenance of cell viability and cooperated with ST to promote gene expression in MCC cell lines. A genome-wide CRISPR-Cas9 screen confirmed the requirement for MYCL and EP400 in MCPyV-positive MCC cell lines. We demonstrate that ST can activate gene expression in a EP400 and MYCL dependent manner and this activity contributes to cellular transformation and generation of induced pluripotent stem cells.
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Affiliation(s)
- Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donglim Esther Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Christian Berrios
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Elizabeth A. White
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Reety Arora
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Rosa Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Timothy Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Thomas Westerling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexander Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Benjamin Strober
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Selene K. Swanson
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter M. Howley
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Megha Padi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - James A. DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Poole CJ, van Riggelen J. MYC-Master Regulator of the Cancer Epigenome and Transcriptome. Genes (Basel) 2017; 8:genes8050142. [PMID: 28505071 PMCID: PMC5448016 DOI: 10.3390/genes8050142] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 01/03/2023] Open
Abstract
Overexpression of MYC is a hallmark of many human cancers. The MYC oncogene has long been thought to execute its neoplastic functions by acting as a classic transcription factor, deregulating the expression of a large number of specific target genes. However, MYC’s influence on many of these target genes is rather modest and there is little overlap between MYC regulated genes in different cell types, leaving many mechanistic questions unanswered. Recent advances in the field challenge the dogma further, revealing a role for MYC that extends beyond the traditional concept of a sequence-specific transcription factor. In this article, we review MYC’s function as a regulator of the cancer epigenome and transcriptome. We outline our current understanding of how MYC regulates chromatin structure in both a site-specific and genome-wide fashion, and highlight the implications for therapeutic strategies for cancers with high MYC expression.
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Affiliation(s)
- Candace J Poole
- Augusta University, Department of Biochemistry and Molecular Biology, 1410 Laney-Walker Blvd., Augusta, GA 30912, USA.
| | - Jan van Riggelen
- Augusta University, Department of Biochemistry and Molecular Biology, 1410 Laney-Walker Blvd., Augusta, GA 30912, USA.
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34
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Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Nature 2017; 544:235-239. [PMID: 28406212 PMCID: PMC5600291 DOI: 10.1038/nature22034] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/05/2017] [Indexed: 02/02/2023]
Abstract
A major goal of biomedicine is to understand the function of every gene in the human genome. Loss-of-function mutations can disrupt both copies of a given gene in humans and phenotypic analysis of such 'human knockouts' can provide insight into gene function. Consanguineous unions are more likely to result in offspring carrying homozygous loss-of-function mutations. In Pakistan, consanguinity rates are notably high. Here we sequence the protein-coding regions of 10,503 adult participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS), designed to understand the determinants of cardiometabolic diseases in individuals from South Asia. We identified individuals carrying homozygous predicted loss-of-function (pLoF) mutations, and performed phenotypic analysis involving more than 200 biochemical and disease traits. We enumerated 49,138 rare (<1% minor allele frequency) pLoF mutations. These pLoF mutations are estimated to knock out 1,317 genes, each in at least one participant. Homozygosity for pLoF mutations at PLA2G7 was associated with absent enzymatic activity of soluble lipoprotein-associated phospholipase A2; at CYP2F1, with higher plasma interleukin-8 concentrations; at TREH, with lower concentrations of apoB-containing lipoprotein subfractions; at either A3GALT2 or NRG4, with markedly reduced plasma insulin C-peptide concentrations; and at SLC9A3R1, with mediators of calcium and phosphate signalling. Heterozygous deficiency of APOC3 has been shown to protect against coronary heart disease; we identified APOC3 homozygous pLoF carriers in our cohort. We recruited these human knockouts and challenged them with an oral fat load. Compared with family members lacking the mutation, individuals with APOC3 knocked out displayed marked blunting of the usual post-prandial rise in plasma triglycerides. Overall, these observations provide a roadmap for a 'human knockout project', a systematic effort to understand the phenotypic consequences of complete disruption of genes in humans.
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Abstract
Although most people still associate actin mainly with the cytoskeleton, several lines of evidence, with the earliest studies dating back to decades ago, have emphasized the importance of actin also inside the cell nucleus. Actin has been linked to many gene expression processes from gene activation to chromatin remodeling, but also to maintenance of genomic integrity and intranuclear movement of chromosomes and chromosomal loci. Recent advances in visualizing different forms and dynamic properties of nuclear actin have clearly advanced our understanding of the basic concepts by which actin operates in the nucleus. In this chapter we address the different breakthroughs in nuclear actin studies, as well as discuss the regulation nuclear actin and the importance of nuclear actin dynamics in relation to its different nuclear functions. Our aim is to highlight the fact that actin should be considered as an essential component of the cell nucleus, and its nuclear actions should be taken into account also in experiments on cytoplasmic actin networks.
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Affiliation(s)
- Tiina Viita
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 56, Helsinki, Finland
| | - Maria K Vartiainen
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 56, Helsinki, Finland.
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36
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Wu S, Yang Z, Ye R, An D, Li C, Wang Y, Wang Y, Huang Y, Liu H, Li F, He L, Sun D, Yu Y, Li Q, Huang P, Zhang M, Zhao X, Bi T, Zhuang X, Zhang L, Lu J, Sun X, Zhou F, Liu C, Yang G, Hou Y, Fan Z, Cai Z. Novel variants in MLL confer to bladder cancer recurrence identified by whole-exome sequencing. Oncotarget 2016; 7:2629-45. [PMID: 26625313 PMCID: PMC4823060 DOI: 10.18632/oncotarget.6380] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
Bladder cancer (BC) is distinguished by high rate of recurrence after surgery, but the underlying mechanisms remain poorly understood. Here we performed the whole-exome sequencing of 37 BC individuals including 20 primary and 17 recurrent samples in which the primary and recurrent samples were not from the same patient. We uncovered that MLL, EP400, PRDM2, ANK3 and CHD5 exclusively altered in recurrent BCs. Specifically, the recurrent BCs and bladder cancer cells with MLL mutation displayed increased histone H3 tri-methyl K4 (H3K4me3) modification in tissue and cell levels and showed enhanced expression of GATA4 and ETS1 downstream. What's more, MLL mutated bladder cancer cells obtained with CRISPR/Cas9 showed increased ability of drug-resistance to epirubicin (a chemotherapy drug for bladder cancer) than wild type cells. Additionally, the BC patients with high expression of GATA4 and ETS1 significantly displayed shorter lifespan than patients with low expression. Our study provided an overview of the genetic basis of recrudescent bladder cancer and discovered that genetic alterations of MLL were involved in BC relapse. The increased modification of H3K4me3 and expression of GATA4 and ETS1 would be the promising targets for the diagnosis and therapy of relapsed bladder cancer.
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Affiliation(s)
- Song Wu
- The Affiliated Luohu Hospital of Shenzhen University, Shenzhen Luohu Hospital Group, Shenzhen, China.,Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhao Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui Ye
- BGI-Shenzhen, Shenzhen, China
| | - Dan An
- BGI-Shenzhen, Shenzhen, China
| | - Chong Li
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yitian Wang
- Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Anhui Medical University, Hefei, China
| | - Yongqiang Wang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Huang
- Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | | | | | - Luyun He
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Da Sun
- BGI-Shenzhen, Shenzhen, China
| | - Yuan Yu
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | | | | | | | | | - Jingxiao Lu
- Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xiaojuan Sun
- Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Fangjian Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunxiao Liu
- Department of Urology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Guosheng Yang
- Guangdong Second People's Hospital, Guangzhou, China
| | | | - Zusen Fan
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhiming Cai
- Department of Urological Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Anhui Medical University, Hefei, China
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37
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Smith RJ, Savoian MS, Weber LE, Park JH. Ataxia telangiectasia mutated (ATM) interacts with p400 ATPase for an efficient DNA damage response. BMC Mol Biol 2016; 17:22. [PMID: 27814680 PMCID: PMC5097431 DOI: 10.1186/s12867-016-0075-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 10/29/2016] [Indexed: 11/13/2022] Open
Abstract
Background Ataxia telangiectasia mutated (ATM) and TRRAP proteins belong to the phosphatidylinositol 3-kinase-related kinase family and are involved in DNA damage repair and chromatin remodeling. ATM is a checkpoint kinase that is recruited to sites of DNA double-strand breaks where it phosphorylates a diverse range of proteins that are part of the chromatin and DNA repair machinery. As an integral subunit of the TRRAP-TIP60 complexes, p400 ATPase is a chromatin remodeler that is also targeted to DNA double-strand break sites. While it is understood that DNA binding transcriptional activators recruit p400 ATPase into a regulatory region of the promoter, how p400 recognises and moves to DNA double-strand break sites is far less clear. Here we investigate a possibility whether ATM serves as a shuttle to deliver p400 to break sites. Results Our data indicate that p400 co-immunoprecipitates with ATM independently of DNA damage state and that the N-terminal domain of p400 is vital for this interaction. Heterologous expression studies using Sf9 cells revealed that the ATM-p400 complex can be reconstituted without other mammalian bridging proteins. Overexpression of ATM-interacting p400 regions in U2OS cells induced dominant negative effects including the inhibition of both DNA damage repair and cell proliferation. Consistent with the dominant negative effect, the stable expression of an N-terminal p400 fragment showed a decrease in the association of p400 with ATM, but did not alter the association of p400 with TRRAP. Conclusion Taken together, our findings suggest that a protein–protein interaction between ATM and p400 ATPase occurs independently of DNA damage and contributes to efficient DNA damage response and repair. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0075-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebecca J Smith
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Matthew S Savoian
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lauren E Weber
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jeong Hyeon Park
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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38
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Zhao LJ, Loewenstein PM, Green M. Ad E1A 243R oncoprotein promotes association of proto-oncogene product MYC with the NuA4/Tip60 complex via the E1A N-terminal repression domain. Virology 2016; 499:178-184. [PMID: 27664947 DOI: 10.1016/j.virol.2016.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/06/2016] [Indexed: 11/25/2022]
Abstract
The adenovirus E1A 243R oncoprotein targets TRRAP, a scaffold protein that assembles histone acetyltransferase (HAT) complexes, such as the NuA4/Tip60 complex which mediates transcriptional activity of the proto-oncogene MYC and helps determine the cancer cell phenotype. How E1A transforms cells through TRRAP remains obscure. We performed proteomic analysis with the N-terminal transcriptional repression domain of E1A 243R (E1A 1-80) and showed that E1A 1-80 interacts with TRRAP, p400, and three other members of the NuA4 complex - DMAP1, RUVBL1 and RUVBL2 - not previously shown to associate with E1A 243R. E1A 1-80 interacts with these NuA4 components and MYC through the E1A TRRAP-targeting domain. E1A 243R association with the NuA4 complex was demonstrated by co-immunoprecipitation and analysis with DMAP1, Tip60, and MYC. Significantly, E1A 243R promotes association of MYC/MAX with the NuA4/Tip60 complex, implicating the importance of the MYC/NuA4 pathway in cellular transformation by both MYC and E1A.
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Affiliation(s)
- Ling-Jun Zhao
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, MO 63104, USA
| | - Paul M Loewenstein
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, MO 63104, USA
| | - Maurice Green
- Department of Microbiology and Molecular Immunology/Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, MO 63104, USA.
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39
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Banerjee Mustafi S, Chakraborty PK, Naz S, Dwivedi SKD, Street M, Basak R, Yang D, Ding K, Mukherjee P, Bhattacharya R. MDR1 mediated chemoresistance: BMI1 and TIP60 in action. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:983-93. [PMID: 27295567 PMCID: PMC4958591 DOI: 10.1016/j.bbagrm.2016.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
Chemotherapy-induced emergence of drug resistant cells is frequently observed and is exemplified by the expression of family of drug resistance proteins including, multidrug resistance protein 1 (MDR1). However, a concise mechanism for chemotherapy-induced MDR1 expression is unclear. Mechanistically, mutational selection, epigenetic alteration, activation of the Wnt pathway or impaired p53 function have been implicated. The present study describes that the surviving fraction of cisplatin resistant cells co- upregulate MDR1, BMI1 and acetyl transferase activity of TIP60. Using complementary gain and loss of function approaches, we demonstrate that the expression of MDR1 is positively regulated by BMI1, a stem-cell factor classically known as a transcriptional repressor. Our study establishes a functional interaction between TIP60 and BMI-1 resulting in upregulation of MDR1 expression. Chromatin immunoprecipitation (ChIP) assays further establish that the proximal MDR1 promoter responds to cisplatin in a BMI1 dependent manner. BMI1 interacts with a cluster of E-box elements on the MDR1 promoter and recruits TIP60 resulting in acetylation of histone H2A and H3. Collectively, our data establish a hitherto unknown liaison among MDR1, BMI1 and TIP60 and provide mechanistic insights into cisplatin-induced MDR1 expression resulting in acquired cross-resistance against paclitaxel, doxorubicin and likely other drugs. In conclusion, our results advocate utilizing anti-BMI1 strategies to alleviate acquired resistance to chemotherapy.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B/agonists
- ATP Binding Cassette Transporter, Subfamily B/genetics
- ATP Binding Cassette Transporter, Subfamily B/metabolism
- Acetylation/drug effects
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- Cisplatin/pharmacology
- Doxorubicin/pharmacology
- Drug Resistance, Multiple/drug effects
- Drug Resistance, Multiple/genetics
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Epithelial Cells/drug effects
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Histone Acetyltransferases/genetics
- Histone Acetyltransferases/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Lysine Acetyltransferase 5
- Paclitaxel/pharmacology
- Polycomb Repressive Complex 1/agonists
- Polycomb Repressive Complex 1/genetics
- Polycomb Repressive Complex 1/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Signal Transduction
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Affiliation(s)
- Soumyajit Banerjee Mustafi
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Prabir Kumar Chakraborty
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Sarwat Naz
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Shailendra Kumar Dhar Dwivedi
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Mark Street
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Rumki Basak
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA; Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kai Ding
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Priyabrata Mukherjee
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Resham Bhattacharya
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA; Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, OK, USA
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40
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Zhao LJ, Loewenstein PM, Green M. The adenoviral E1A N-terminal domain represses MYC transcription in human cancer cells by targeting both p300 and TRRAP and inhibiting MYC promoter acetylation of H3K18 and H4K16. Genes Cancer 2016; 7:98-109. [PMID: 27382434 PMCID: PMC4918948 DOI: 10.18632/genesandcancer.99] [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] [Indexed: 12/22/2022] Open
Abstract
Human cancers frequently arise from increased expression of proto-oncogenes, such as MYC and HER2. Understanding the cellular pathways regulating the transcription and expression of proto-oncogenes is important for targeted therapies for cancer treatment. Adenoviral (Ad) E1A 243R (243 aa residues) is a viral oncoprotein that interacts with key regulators of gene transcription and cell proliferation. We have shown previously that the 80 amino acid N-terminal transcriptional repression domain of E1A 243R (E1A 1-80) can target the histone acetyltransferase (HAT) p300 and repress HER2 in the HER2-overexpressing human breast cancer cell line SKBR3. Expression of E1A 1-80 induces death of SKBR3 and other cancer cell lines. In this study, we performed total cell RNA sequence analysis and identified MYC as the regulatory gene for cellular proliferation most strongly repressed by E1A 1-80. By RT-quantitative PCR analysis we show that repression of MYC in SKBR3 cells occurs early after expression of E1A 1-80, suggesting that MYC may be an early responder of E1A 1-80-mediated transcriptional repression. Of interest, while E1A 1-80 repression of MYC occurs in all eight human cancer cell lines examined, repression of HER2 is cell-type dependent. We demonstrate by ChIP analysis that MYC transcriptional repression by E1A 1-80 is associated with inhibition of acetylation of H3K18 and H4K16 on the MYC promoter, as well as inhibition of RNA Pol II binding to the MYC promoter. Deletion mutant analysis of E1A 1-80 suggests that both p300/CBP and TRRAP are involved in E1A 1-80 repression of MYC transcription. Further, E1A 1-80 interaction with p300/CBP and TRRAP is correlated with inhibition of H3K18 and H4K16 acetylation on the MYC promoter, respectively. Our results indicate that E1A 1-80 may target two important pathways for histone modification to repress transcription in human cancer cells.
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Affiliation(s)
- Ling-Jun Zhao
- Institute for Molecular Virology, Department of Microbiology and Molecular Immunology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | - Paul M Loewenstein
- Institute for Molecular Virology, Department of Microbiology and Molecular Immunology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | - Maurice Green
- Institute for Molecular Virology, Department of Microbiology and Molecular Immunology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
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41
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A Role for Nuclear Actin in HDAC 1 and 2 Regulation. Sci Rep 2016; 6:28460. [PMID: 27345839 PMCID: PMC4921920 DOI: 10.1038/srep28460] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 05/26/2016] [Indexed: 01/13/2023] Open
Abstract
Class I histone deacetylases (HDACs) are known to remove acetyl groups from histone tails. This liberates positive charges on the histone tail and allows for tighter winding of DNA, preventing transcription factor binding and gene activation. Although the functions of HDAC proteins are becoming apparent both biochemically and clinically, how this class of proteins is regulated remains poorly understood. We identified a novel interaction between nuclear actin and HDAC 1 and HDAC 2. Nuclear actin has been previously shown to interact with a growing list of nuclear proteins including chromatin remodeling complexes, transcription factors and RNA polymerases. We find that monomeric actin is able to bind the class I HDAC complex. Furthermore, increasing the concentration of actin in HeLa nuclear extracts was able to suppress overall HDAC function. Conversely, polymerizing nuclear actin increased HDAC activity and decreased histone acetylation. Moreover, the interaction between class I HDACs and nuclear actin was found to be activity dependent. Together, our data suggest nuclear actin is able to regulate HDAC 1 and 2 activity.
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42
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Beaulieu YB, Leon Machado JA, Ethier S, Gaudreau L, Steimle V. Degradation, Promoter Recruitment and Transactivation Mediated by the Extreme N-Terminus of MHC Class II Transactivator CIITA Isoform III. PLoS One 2016; 11:e0148753. [PMID: 26871568 PMCID: PMC4752451 DOI: 10.1371/journal.pone.0148753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
Multiple relationships between ubiquitin-proteasome mediated protein turnover and transcriptional activation have been well documented, but the underlying mechanisms are still poorly understood. One way to induce degradation is via ubiquitination of the N-terminal α-amino group of proteins. The major histocompatibility complex (MHC) class II transactivator CIITA is the master regulator of MHC class II gene expression and we found earlier that CIITA is a short-lived protein. Using stable and transient transfections of different CIITA constructs into HEK-293 and HeLa cell lines, we show here that the extreme N-terminal end of CIITA isoform III induces both rapid degradation and transactivation. It is essential that this sequence resides at the N-terminal end of the protein since blocking of the N-terminal end with an epitope-tag stabilizes the protein and reduces transactivation potential. The first ten amino acids of CIITA isoform III act as a portable degron and transactivation sequence when transferred as N-terminal extension to truncated CIITA constructs and are also able to destabilize a heterologous protein. The same is observed with the N-terminal ends of several known N-terminal ubiquitination substrates, such as Id2, Cdt1 and MyoD. Arginine and proline residues within the N-terminal ends contribute to rapid turnover. The N-terminal end of CIITA isoform III is responsible for efficient in vivo recruitment to the HLA-DRA promoter and increased interaction with components of the transcription machinery, such as TBP, p300, p400/Domino, the 19S ATPase S8, and the MHC-II promoter binding complex RFX. These experiments reveal a novel function of free N-terminal ends of proteins in degradation-dependent transcriptional activation.
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Affiliation(s)
- Yves B. Beaulieu
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | | | - Sylvain Ethier
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Luc Gaudreau
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Viktor Steimle
- Département de biologie, Université de Sherbrooke, Sherbrooke, Qc, Canada
- * E-mail:
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Judes G, Rifaï K, Ngollo M, Daures M, Bignon YJ, Penault-Llorca F, Bernard-Gallon D. A bivalent role of TIP60 histone acetyl transferase in human cancer. Epigenomics 2015; 7:1351-63. [PMID: 26638912 DOI: 10.2217/epi.15.76] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Acetylation is a major modification that is required for gene regulation, genome maintenance and metabolism. A dysfunctional acetylation plays an important role in several diseases, including cancer. A group of enzymes-lysine acetyltransferases are responsible for this modification and act in regulation of transcription as cofactors and by acetylation of histones and other proteins. Tip60, a member of MYST family, is expressed ubiquitously and is the acetyltransferase catalytic subunit of human NuA4 complex. This HAT has a well-characterized involvement in many processes, such as cellular signaling, DNA damage repair, transcriptional and cellular cycle. Aberrant lysine acetyltransferase functions promote or suppress tumorigenesis in different cancers such as colon, breast and prostate tumors. Therefore, Tip60 might be a potential and important therapeutic target in the cancer treatment; new histone acetyl transferase inhibitors were identified and are more selective inhibitors of Tip60.
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Affiliation(s)
- Gaëlle Judes
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
| | - Khaldoun Rifaï
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
| | - Marjolaine Ngollo
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
| | - Marine Daures
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
| | - Frédérique Penault-Llorca
- EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France.,Centre Jean Perrin, Laboratory of Biopathology, 63011 Clermont-Ferrand, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, 63001 Clermont-Ferrand, France.,EA 4677 'ERTICA', University of Auvergne, 63011 Clermont-Ferrand, France
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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.
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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.
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The Cellular Protein Complex Associated with a Transforming Region of E1A Contains c-MYC. J Virol 2015; 90:1070-9. [PMID: 26559831 DOI: 10.1128/jvi.02039-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The cell-transforming activity of human adenovirus 5 (hAd5) E1A is mediated by the N-terminal half of E1A, which interacts with three different major cellular protein complexes, p300/CBP, TRRAP/p400, and pRb family members. Among these protein interactions, the interaction of pRb family proteins with conserved region 2 (CR2) of E1A is known to promote cell proliferation by deregulating the activities of E2F family transcription factors. The functional consequences of interaction with the other two protein complexes in regulating the transforming activity of E1A are not well defined. Here, we report that the E1A N-terminal region also interacted with the cellular proto-oncoprotein c-MYC and the homolog of enhancer of yellow 2 (ENY2). Our results suggested that these proteins interacted with an essential E1A transforming domain spanning amino acid residues 26 to 35 which also interacted with TRRAP and p400. Small interfering RNA (siRNA)-mediated depletion of TRRAP reduced c-MYC interaction with E1A, while p400 depletion did not. In contrast, depletion of TRRAP enhanced ENY2 interaction with E1A, suggesting that ENY2 and TRRAP may interact with E1A in a competitive manner. The same E1A region additionally interacted with the constituents of a deubiquitinase complex consisting of USP22, ATXN7, and ATXN7L3 via TRRAP. Acute short hairpin RNA (shRNA)-mediated depletion of c-MYC reduced the E1A transforming activity, while depletion of ENY2 and MAX did not. These results suggested that the association of c-MYC with E1A may, at least partially, play a role in the E1A transformation activity, independently of MAX. IMPORTANCE The transforming region of adenovirus E1A consists of three short modules which complex with different cellular protein complexes. The mechanism by which one of the transforming modules, CR2, promotes cell proliferation, through inactivating the activities of the pRb family proteins, is better understood than the activities of the other domains. Our analysis of the E1A proteome revealed the presence of the proto-oncoprotein c-MYC and of ENY2. We mapped these interactions to a critical transforming module of E1A that was previously known to interact with the scaffolding molecule TRRAP and the E1A-binding protein p400. We showed that c-MYC interacted with E1A through TRRAP, while ENY2 interacted with it independently. The data reported here indicated that depletion of c-MYC in normal human cells reduced the transforming activity of E1A. Our result raises a novel paradigm in oncogenic transformation by a DNA viral oncogene, the E1A gene, that may exploit the activity of a cellular oncogene, the c-MYC gene, in addition to inactivation of the tumor suppressors, such as pRb.
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Ravens S, Yu C, Ye T, Stierle M, Tora L. Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells. Epigenetics Chromatin 2015; 8:45. [PMID: 26550034 PMCID: PMC4636812 DOI: 10.1186/s13072-015-0039-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/29/2015] [Indexed: 01/24/2023] Open
Abstract
Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0039-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarina Ravens
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Changwei Yu
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Tao Ye
- Microarrays and Deep Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, UdS, BP 10142, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Matthieu Stierle
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Laszlo Tora
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
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Dalvai M, Loehr J, Jacquet K, Huard CC, Roques C, Herst P, Côté J, Doyon Y. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells. Cell Rep 2015; 13:621-633. [PMID: 26456817 DOI: 10.1016/j.celrep.2015.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 07/27/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022] Open
Abstract
Conventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.
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Affiliation(s)
- Mathieu Dalvai
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Karine Jacquet
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Caroline C Huard
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Céline Roques
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Pauline Herst
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Jacques Côté
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada.
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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Falahzadeh K, Banaei-Esfahani A, Shahhoseini M. The potential roles of actin in the nucleus. CELL JOURNAL 2015; 17:7-14. [PMID: 25870830 PMCID: PMC4393673 DOI: 10.22074/cellj.2015.507] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 11/05/2013] [Indexed: 11/16/2022]
Abstract
Over the past few decades, actin’s presence in the nucleus has been demonstrated. Actin
is a key protein necessary for different nuclear processes. Although actin is well known for
its functional role in dynamic behavior of the cytoskeleton, emerging studies are now highlighting new roles for actin. At the present time there is no doubt about the presence of actin in the nucleus. A number of studies have uncovered the functional involvement of actin
in nuclear processes. Actin as one of the nuclear components has its own structured and
functional rules, such as nuclear matrix association, chromatin remodeling, transcription
by RNA polymerases I, II, III and mRNA processing. In this historical review, we attempt to
provide an overview of our current understanding of the functions of actin in the nucleus.
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Affiliation(s)
- Khadijeh Falahzadeh
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran ; Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University (TMU), Tehran, Iran
| | - Amir Banaei-Esfahani
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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50
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Fluctuating expression of microRNAs in adenovirus infected cells. Virology 2015; 478:99-111. [PMID: 25744056 DOI: 10.1016/j.virol.2015.01.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/20/2015] [Accepted: 01/23/2015] [Indexed: 12/15/2022]
Abstract
The changes in cellular microRNA (miRNA) expression during the course of an adenovirus type 2 infection in human lung fibroblast were studied by deep RNA sequencing. Expressions of 175 miRNAs with over 100 transcripts per million nucleotides were changed more than 1.5-fold. The expression patterns of these miRNAs changed dramatically during the course of the infection, from upregulation of the miRNAs known as tumor suppressors (such as miR-22, miR-320, let-7, miR-181b, and miR-155) and down-regulation of oncogenic miRNAs (such as miR-21 and miR-31) early to downregulation of tumor suppressor miRNAs (such as let-7 family, mir-30 family, 23/27 cluster) and upregulation of oncogenic miRNAs (include miR-125, miR-27, miR-191) late after infection. The switch in miRNA expression pattern occurred when adenovirus DNA replication started. Furthermore, deregulation of cellular miRNA expression was a step-wise and special sets of miRNAs were deregulated in different phases of infection.
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