1
|
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
Collapse
Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
| |
Collapse
|
2
|
Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science 2019; 365:365/6452/eaaw4361. [PMID: 31371577 DOI: 10.1126/science.aaw4361] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 12/11/2022]
Abstract
Laboratory mouse studies are paramount for understanding basic biological phenomena but also have limitations. These include conflicting results caused by divergent microbiota and limited translational research value. To address both shortcomings, we transferred C57BL/6 embryos into wild mice, creating "wildlings." These mice have a natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6 mice. The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multiple organs. Their gut microbiota outcompete laboratory microbiota and demonstrate resilience to environmental challenges. Wildlings, but not conventional laboratory mice, phenocopied human immune responses in two preclinical studies. A combined natural microbiota- and pathogen-based model may enhance the reproducibility of biomedical studies and increase the bench-to-bedside safety and success of immunological studies.
Collapse
Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Jasmin Herz
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Brian G Vassallo
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Ashli Hunter
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Morgan K Wall
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Irina Leonardi
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nicholas Collins
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Blatter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong-Ji Han
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana Potapova
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Mark B Foster St Claire
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Wuxing Yuan
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shurjo K Sen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew S Dreier
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| |
Collapse
|
3
|
Muys BR, Sousa JF, Plaça JR, de Araújo LF, Sarshad AA, Anastasakis DG, Wang X, Li XL, de Molfetta GA, Ramão A, Lal A, Vidal DO, Hafner M, Silva WA. miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism. Cancer Res 2019; 79:3294-3305. [PMID: 31101765 DOI: 10.1158/0008-5472.can-19-0490] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 01/17/2023]
Abstract
Dysregulation of miRNA expression is associated with multiple diseases, including cancers, in which small RNAs can have either oncogenic or tumor suppressive functions. Here we investigated the potential tumor suppressive function of miR-450a, one of the most significantly downregulated miRNAs in ovarian cancer. RNA-seq analysis of the ovarian cancer cell line A2780 revealed that overexpression of miR-450a suppressed multiple genes involved in the epithelial-to-mesenchymal transition (EMT). Overexpression of miR-450a reduced tumor migration and invasion and increased anoikis in A2780 and SKOV-3 cell lines and reduced tumor growth in an ovarian tumor xenographic model. Combined AGO-PAR-CLIP and RNA-seq analysis identified a panel of potential miR-450a targets, of which many, including TIMMDC1, MT-ND2, ACO2, and ATP5B, regulate energetic metabolism. Following glutamine withdrawal, miR-450a overexpression decreased mitochondrial membrane potential but increased glucose uptake and viability, characteristics of less invasive ovarian cancer cell lines. In summary, we propose that miR-450a acts as a tumor suppressor in ovarian cancer cells by modulating targets associated with glutaminolysis, which leads to decreased production of lipids, amino acids, and nucleic acids, as well as inhibition of signaling pathways associated with EMT. SIGNIFICANCE: miR-450a limits the metastatic potential of ovarian cancer cells by targeting a set of mitochondrial mRNAs to reduce glycolysis and glutaminolysis.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/13/3294/F1.large.jpg.
Collapse
Affiliation(s)
- Bruna Rodrigues Muys
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland.,Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Josane F Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Genetics and Molecular Biology Program, Institute of Biological Sciences, Federal University of Para-UFPA, Belem, Brazil
| | - Jessica Rodrigues Plaça
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| | - Luíza Ferreira de Araújo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Medical Genomics Laboratory, AC Camargo Cancer Center, São Paulo, Brazil
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Greice Andreotti de Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Daniel Onofre Vidal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland.
| | - Wilson A Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil. .,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| |
Collapse
|
4
|
Gao QQ, Putzbach WE, Murmann AE, Chen S, Sarshad AA, Peter JM, Bartom ET, Hafner M, Peter ME. 6mer seed toxicity in tumor suppressive microRNAs. Nat Commun 2018; 9:4504. [PMID: 30374110 PMCID: PMC6206098 DOI: 10.1038/s41467-018-06526-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022] Open
Abstract
Many small-interfering (si)RNAs are toxic to cancer cells through a 6mer seed sequence (positions 2–7 of the guide strand). Here we performed an siRNA screen with all 4096 6mer seeds revealing a preference for guanine in positions 1 and 2 and a high overall G or C content in the seed of the most toxic siRNAs for four tested human and mouse cell lines. Toxicity of these siRNAs stems from targeting survival genes with C-rich 3′UTRs. The master tumor suppressor miRNA miR-34a-5p is toxic through such a G-rich 6mer seed and is upregulated in cells subjected to genotoxic stress. An analysis of all mature miRNAs suggests that during evolution most miRNAs evolved to avoid guanine at the 5′ end of the 6mer seed sequence of the guide strand. In contrast, for certain tumor-suppressive miRNAs the guide strand contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells. Small interfering (siRNAs) can be toxic to cancer cells. Here the authors investigate the toxicity of microRNA in cancer cells by performing a siRNA screen that tests the miRNA activities of an extensive list of miRNAs with different 6mer seed sequences.
Collapse
Affiliation(s)
- Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - William E Putzbach
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, NIH, Bethesda, MD, 20892, USA
| | | | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, NIH, Bethesda, MD, 20892, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA. .,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA.
| |
Collapse
|
5
|
Putzbach W, Haluck-Kangas A, Gao QQ, Sarshad AA, Bartom ET, Stults A, Qadir AS, Hafner M, Peter ME. CD95/Fas ligand mRNA is toxic to cells. eLife 2018; 7:38621. [PMID: 30324908 PMCID: PMC6191286 DOI: 10.7554/elife.38621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/15/2018] [Indexed: 12/21/2022] Open
Abstract
CD95/Fas ligand binds to the death receptor CD95 to induce apoptosis in sensitive cells. We previously reported that CD95L mRNA is enriched in sequences that, when converted to si/shRNAs, kill all cancer cells by targeting critical survival genes (Putzbach et al., 2017). We now report expression of full-length CD95L mRNA itself is highly toxic to cells and induces a similar form of cell death. We demonstrate that small (s)RNAs derived from CD95L are loaded into the RNA induced silencing complex (RISC) which is required for the toxicity and processing of CD95L mRNA into sRNAs is independent of both Dicer and Drosha. We provide evidence that in addition to the CD95L transgene a number of endogenous protein coding genes involved in regulating protein translation, particularly under low miRNA conditions, can be processed to sRNAs and loaded into the RISC suggesting a new level of cell fate regulation involving RNAi.
Collapse
Affiliation(s)
- Will Putzbach
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Ashley Haluck-Kangas
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Austin Stults
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Abdul S Qadir
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| |
Collapse
|
6
|
Sarshad AA, Juan AH, Muler AIC, Anastasakis DG, Wang X, Genzor P, Feng X, Tsai PF, Sun HW, Haase AD, Sartorelli V, Hafner M. Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells. Mol Cell 2018; 71:1040-1050.e8. [PMID: 30146314 PMCID: PMC6690358 DOI: 10.1016/j.molcel.2018.07.020] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/12/2018] [Accepted: 07/17/2018] [Indexed: 01/13/2023]
Abstract
In mammals, gene silencing by the RNA-induced silencing complex (RISC) is a well-understood cytoplasmic posttranscriptional gene regulatory mechanism. Here, we show that embryonic stem cells (ESCs) contain high levels of nuclear AGO proteins and that in ESCs nuclear AGO protein activity allows for the onset of differentiation. In the nucleus, AGO proteins interact with core RISC components, including the TNRC6 proteins and the CCR4-NOT deadenylase complex. In contrast to cytoplasmic miRNA-mediated gene silencing that mainly operates on cis-acting elements in mRNA 3' untranslated (UTR) sequences, in the nucleus AGO binding in the coding sequence and potentially introns also contributed to post-transcriptional gene silencing. Thus, nuclear localization of AGO proteins in specific cell types leads to a previously unappreciated expansion of the miRNA-regulated transcriptome.
Collapse
Affiliation(s)
- Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Ana Iris Correa Muler
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Pavol Genzor
- Laboratory of Biochemistry and Molecular Biology, National Institute for Diabetes and Digestive and Kidney Diseases, 8 Center Drive, Bethesda, MD 20892, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Pei-Fang Tsai
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA
| | - Astrid D Haase
- Laboratory of Biochemistry and Molecular Biology, National Institute for Diabetes and Digestive and Kidney Diseases, 8 Center Drive, Bethesda, MD 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA.
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, 50 South Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
7
|
Tsai PF, Dell'Orso S, Rodriguez J, Vivanco KO, Ko KD, Jiang K, Juan AH, Sarshad AA, Vian L, Tran M, Wangsa D, Wang AH, Perovanovic J, Anastasakis D, Ralston E, Ried T, Sun HW, Hafner M, Larson DR, Sartorelli V. A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans. Mol Cell 2018; 71:129-141.e8. [PMID: 29979962 PMCID: PMC6082425 DOI: 10.1016/j.molcel.2018.06.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/19/2018] [Accepted: 06/01/2018] [Indexed: 12/16/2022]
Abstract
The enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. Core enhancer eRNA (CEeRNA) regulates transcription of the adjacent MyoD gene, whereas DRReRNA affects expression of Myogenin in trans. We found that DRReRNA is recruited at the Myogenin locus, where it colocalizes with Myogenin nascent transcripts. DRReRNA associates with the cohesin complex, and this association correlates with its transactivating properties. Despite being expressed in undifferentiated cells, cohesin is not loaded on Myogenin until the cells start expressing DRReRNA, which is then required for cohesin chromatin recruitment and maintenance. Functionally, depletion of either cohesin or DRReRNA reduces chromatin accessibility, prevents Myogenin activation, and hinders muscle cell differentiation. Thus, DRReRNA ensures spatially appropriate cohesin loading in trans to regulate gene expression.
Collapse
Affiliation(s)
- Pei-Fang Tsai
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Stefania Dell'Orso
- High-Throughput Sequencing Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Joseph Rodriguez
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Karinna O Vivanco
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Kyung-Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Laura Vian
- Translational Immunology Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Michelle Tran
- Light Imaging Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - A Hongjun Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Dimitrios Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Evelyn Ralston
- Light Imaging Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
8
|
Gao QQ, Putzbach WT, Murmann AE, Chen S, Sarshad AA, Ambrosini G, Bartom ET, Hafner M, Peter ME. Abstract LB-401: Induction of DISE by tumor suppressive microRNAs. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many siRNAs and shRNAs induce a form of cell death in all cancer cells that involves silencing a set of critical survival genes, a process called death induced by survival gene elimination (DISE). Mechanistically a 6mer seed sequence (position 2-7 of the guide strand) is sufficient to confer DISE-inducing activity. We have now performed a strand specific screen testing the toxicity of all 4096 possible 6mer seed sequences in a neutral double stranded siRNA backbone. We found an asymmetric preference for guanine in positions 1-3 of the 6mer seed in the most toxic siRNAs which target survival genes that are GC rich in their 3'UTR. During over 800 million years of evolution miRNAs have evolved to avoid guanine in their seed sequences. However, two tumor suppressive miRNAs were found to be killing cancer cells through DISE using G rich toxic seeds in cells exposed to genotoxic stress: 1) the p53 inducible miR-34 family and most of its cell death inducing activity comes from its 6mer seed; and 2) miR-320a, a noncanonical miRNA that is still expressed in cancer cells when miRNA processing genes are mutated. Ago bound upregulated miR-320a is converted from a poorly to a highly toxic miRNA by removal of two adenine nucleotides from its 5' end. Our data suggest that most miRNAs have evolved to avoid induction of DISE but certain tumor suppressive miRNAs utilize this mechanism to kill cancer cells.
Citation Format: Quan Q. Gao, William T. Putzbach, Andrea E. Murmann, Siquan Chen, Aishe A. Sarshad, Giovanna Ambrosini, Elizabeth T. Bartom, Markus Hafner, Marcus E. Peter. Induction of DISE by tumor suppressive microRNAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-401.
Collapse
Affiliation(s)
| | | | | | | | | | - Giovanna Ambrosini
- 3Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland
| | | | | | | |
Collapse
|
9
|
Putzbach W, Haluck-Kangas A, Gao Q, Sarshad AA, Bartom E, Stults A, Qadir AS, Scholtens DM, Hafner M, Peter M. Abstract 4391: CD95L mRNA is toxic to cancer cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
CD95/Fas ligand (CD95L) is best characterized for its role in activating extrinsic apoptosis through binding to its receptor, CD95. However, we recently reported that the CD95L mRNA is enriched in sequences that when converted to si- or shRNAs kill cancer cells through an RNAi-dependent mechanism. When loaded into the RNA Induced Silencing Complex (RISC), CD95L-derived small RNAs downregulate genes critical for cancer cell survival, eliciting a unique form of cell death we call Death Induced by Survival Gene Elimination (DISE). We now report that expression of full-length CD95L mRNA itself is toxic to cells. Acute expression of either wild-type CD95L mRNA in CD95-deficient cells or a CD95L mRNA with a premature stop codon in CD95 wild-type cells induces cell death. RNA-Seq analysis of small RNA reveals that CD95L mRNA is specifically processed into discrete clusters ~19-25 nucleotides long that map along the CD95L ORF. These clusters of CD95L sequences were bound by AGO proteins in cells about to die, suggesting that the mRNA may be killing cells through an RNAi-dependent mechanism. Generation of AGO-bound CD95L mRNA sequences does not appear to be dependent on the canonical miRNA biogenesis pathway, as clusters of CD95L mRNA were detectable in both Drosha and Dicer deficient HCT116 cells. We propose that CD95L mRNA is toxic to cells through processing and loading of small CD95L-derived RNA sequences into the RISC.
Citation Format: William Putzbach, Ashley Haluck-Kangas, Quan Gao, Aishe A. Sarshad, Elizabeth Bartom, Austin Stults, Abdul S. Qadir, Denise M. Scholtens, Markus Hafner, Marcus Peter. CD95L mRNA is toxic to cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4391.
Collapse
Affiliation(s)
- William Putzbach
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Quan Gao
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Aishe A. Sarshad
- 2National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD
| | - Elizabeth Bartom
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Austin Stults
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Abdul S. Qadir
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Markus Hafner
- 2National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD
| | - Marcus Peter
- 1Northwestern University Feinberg School of Medicine, Chicago, IL
| |
Collapse
|
10
|
Putzbach W, Gao QQ, Patel M, van Dongen S, Haluck-Kangas A, Sarshad AA, Bartom ET, Kim KYA, Scholtens DM, Hafner M, Zhao JC, Murmann AE, Peter ME. Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism. eLife 2017; 6. [PMID: 29063830 PMCID: PMC5655136 DOI: 10.7554/elife.29702] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 09/13/2017] [Indexed: 12/27/2022] Open
Abstract
Over 80% of multiple-tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death characterized by simultaneous activation of multiple cell death pathways preferentially killing transformed and cancer stem cells. We now show these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect we call DISE (death induced by survival gene elimination). Drosha and Dicer-deficient cells, devoid of most miRNAs, are hypersensitive to DISE, suggesting cellular miRNAs protect cells from this form of cell death. By testing 4666 shRNAs derived from the CD95 and CD95L mRNA sequences and an unrelated control gene, Venus, we have identified many toxic sequences - most of them located in the open reading frame of CD95L. We propose that specific toxic RNAi-active sequences present in the genome can kill cancer cells. Cells store their genetic code within molecules of DNA. Some of this information will be copied into chemically similar molecules called RNAs, from which the sequence of letters in the genetic code can be translated to build proteins. However, these messenger RNAs are not the only RNA molecules that cells can make. MicroRNAs are other short pieces of RNA that closely match sequences in parts of certain messenger RNAs. The messenger RNAs targeted by microRNAs are broken down inside the cell, which reduces how much protein can be produced from them. Since its discovery, scientists have exploited this process – called RNA interference (or RNAi for short) – and designed microRNA-like small interfering RNAs (siRNAs) to target particular messenger RNAs and decrease the levels of the corresponding proteins in countless experiments. Two proteins that have been studied in RNAi experiments are CD95 and its interaction partner CD95L. Both of these proteins are important in human cancer cells, and targeting them via RNAi killed cancer cells in an unknown mechanism that the cancer cells were unable to resist. RNAi experiments are designed to be specific, but sometimes they can accidently target other non-target messenger RNAs. Putzbach, Gao, Patel et al. have now analyzed all of the siRNAs that can be made from the messenger RNAs for CD95 and CD95L to mediate RNAi in cancer cells. This revealed that several messenger RNAs, other than those for CD95 and CD95L, were unintentionally being targeted, including many that code for proteins that cells need to survive. Further examination of the messenger RNA for CD95 and CD95L showed that they contain short sequences that are similar to those in the messenger RNAs of the genes that encode these survival proteins. Putzbach et al. were able to study and then predict which siRNA sequences would be toxic to cancer cells. These findings indicate that an RNAi off-target effect may actually be used to kill cancer cells. Future studies will determine whether this effect could be exploited to shrink tumors in animal models of cancer. If successful, this in turn could lead to new treatments for cancer patients.
Collapse
Affiliation(s)
- William Putzbach
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Quan Q Gao
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Monal Patel
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Stijn van Dongen
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Ashley Haluck-Kangas
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Denise M Scholtens
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Jonathan C Zhao
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Andrea E Murmann
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States
| | - Marcus E Peter
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| |
Collapse
|
11
|
Benhalevy D, McFarland HL, Sarshad AA, Hafner M. PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites. Methods 2016; 118-119:41-49. [PMID: 27871973 DOI: 10.1016/j.ymeth.2016.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/01/2016] [Accepted: 11/16/2016] [Indexed: 10/20/2022] Open
Abstract
The study of protein-RNA interactions is critical for our understanding of cellular processes and regulatory circuits controlled by RNA binding proteins (RBPs). Recent next generation sequencing-based approaches significantly promoted our understanding of RNA biology and its importance for cell function. We present a streamlined protocol for Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a technique that allows for the characterization of RBP binding sites on target RNAs at nucleotide resolution and transcriptome-wide scale. PAR-CLIP involves irreversible UV-mediated crosslinking of RNAs labeled with photoreactive nucleosides to interacting proteins, followed by stringent purification steps and the conversion of crosslinked RNA into small RNA cDNA libraries compatible with next-generation sequencing. The defining hallmark of PAR-CLIP is a diagnostic mutation at the crosslinking site that is introduced into cDNA during the library preparation process. This feature allows for efficient computational removal of contaminating sequences derived from non-crosslinked fragments of abundant cellular RNAs. In the following, we present two different step-by-step procedures for PAR-CLIP, which differ in the small RNA cDNA library preparation procedure: (1) Standard library preparation involving gel size selections after each enzymatic manipulation, and (2) A modified PAR-CLIP procedure ("on-beads" PAR-CLIP), where most RNA manipulations including the necessary adapter ligation steps are performed on the immobilized RNP. This streamlined procedure reduces the protocol preparation time by three days compared to the standard workflow.
Collapse
Affiliation(s)
- Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892, USA
| | - Hannah L McFarland
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
12
|
Dass RA, Sarshad AA, Carson BB, Feenstra JM, Kaur A, Obrdlik A, Parks MM, Prakash V, Love DK, Pietras K, Serra R, Blanchard SC, Percipalle P, Brown AMC, Vincent CT. Wnt5a Signals through DVL1 to Repress Ribosomal DNA Transcription by RNA Polymerase I. PLoS Genet 2016; 12:e1006217. [PMID: 27500936 PMCID: PMC4976976 DOI: 10.1371/journal.pgen.1006217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/05/2016] [Indexed: 11/19/2022] Open
Abstract
Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer. Accordingly, numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis. In breast cancer, non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth. Here, we show that Wnt5a rapidly represses rDNA gene transcription in breast cancer cells and generates a chromatin state with reduced transcription of rDNA by RNA polymerase I (Pol I). These effects were specifically dependent on Dishevelled1 (DVL1), which accumulates in nucleolar organizer regions (NORs) and binds to rDNA regions of the chromosome. Upon DVL1 binding, the Pol I transcription activator and deacetylase Sirtuin 7 (SIRT7) releases from rDNA loci, concomitant with disassembly of Pol I transcription machinery at the rDNA promoter. These findings reveal that Wnt5a signals through DVL1 to suppress rRNA transcription. This provides a novel mechanism for how Wnt5a exerts tumor suppressive effects and why disruption of Wnt5a signaling enhances mammary tumor growth in vivo.
Collapse
Affiliation(s)
- Randall A. Dass
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Aishe A. Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Brittany B. Carson
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Jennifer M. Feenstra
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Amanpreet Kaur
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Ales Obrdlik
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Matthew M. Parks
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Varsha Prakash
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Damon K. Love
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kristian Pietras
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, Sweden
| | - Rosa Serra
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- Tri-Institutional PhD program in Chemical Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- * E-mail: (PP); (AMCB); (CTV)
| | - Anthony M. C. Brown
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (PP); (AMCB); (CTV)
| | - C. Theresa Vincent
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
- * E-mail: (PP); (AMCB); (CTV)
| |
Collapse
|
13
|
Almuzzaini B, Sarshad AA, Rahmanto AS, Hansson ML, Von Euler A, Sangfelt O, Visa N, Farrants AKÖ, Percipalle P. In β-actin knockouts, epigenetic reprogramming and rDNA transcription inactivation lead to growth and proliferation defects. FASEB J 2016; 30:2860-73. [PMID: 27127100 DOI: 10.1096/fj.201600280r] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/18/2016] [Indexed: 12/18/2022]
Abstract
Actin and nuclear myosin 1 (NM1) are regulators of transcription and chromatin organization. Using a genome-wide approach, we report here that β-actin binds intergenic and genic regions across the mammalian genome, associated with both protein-coding and rRNA genes. Within the rDNA, the distribution of β-actin correlated with NM1 and the other subunits of the B-WICH complex, WSTF and SNF2h. In β-actin(-/-) mouse embryonic fibroblasts (MEFs), we found that rRNA synthesis levels decreased concomitantly with drops in RNA polymerase I (Pol I) and NM1 occupancies across the rRNA gene. Reintroduction of wild-type β-actin, in contrast to mutated forms with polymerization defects, efficiently rescued rRNA synthesis underscoring the direct role for a polymerization-competent form of β-actin in Pol I transcription. The rRNA synthesis defects in the β-actin(-/-) MEFs are a consequence of epigenetic reprogramming with up-regulation of the repressive mark H3K4me1 (monomethylation of lys4 on histone H3) and enhanced chromatin compaction at promoter-proximal enhancer (T0 sequence), which disturb binding of the transcription factor TTF1. We propose a novel genome-wide mechanism where the polymerase-associated β-actin synergizes with NM1 to coordinate permissive chromatin with Pol I transcription, cell growth, and proliferation.-Almuzzaini, B., Sarshad, A. A. , Rahmanto, A. S., Hansson, M. L., Von Euler, A., Sangfelt, O., Visa, N., Farrants, A.-K. Ö., Percipalle, P. In β-actin knockouts, epigenetic reprogramming and rDNA transcription inactivation lead to growth and proliferation defects.
Collapse
Affiliation(s)
- Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; and
| | - Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Aldwin S Rahmanto
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Magnus L Hansson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Anne Von Euler
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Neus Visa
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia Division of Science, Department of Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
14
|
Almuzzaini B, Sarshad AA, Farrants AKÖ, Percipalle P. Nuclear myosin 1 contributes to a chromatin landscape compatible with RNA polymerase II transcription activation. BMC Biol 2015; 13:35. [PMID: 26044184 PMCID: PMC4486089 DOI: 10.1186/s12915-015-0147-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/02/2015] [Indexed: 12/11/2022] Open
Abstract
Background Nuclear myosin 1c (NM1) is emerging as a regulator of transcription and chromatin organization. Results Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) in combination with molecular analyses, we investigated the global association of NM1 with the mammalian genome. Analysis of the ChIP-Seq data demonstrates that NM1 binds across the entire mammalian genome with occupancy peaks correlating with distributions of RNA Polymerase II (Pol II) and active epigenetic marks at class II gene promoters. In mouse embryonic fibroblasts subjected to RNAi mediated NM1 gene silencing, we show that NM1 synergizes with polymerase-associated actin to maintain active Pol II at the promoter. NM1 also co-localizes with the nucleosome remodeler SNF2h at class II promoters where they assemble together with WSTF as part of the B-WICH complex. A high resolution micrococcal nuclease (MNase) assay and quantitative real time PCR shows that this mechanism is required for local chromatin remodeling. Following B-WICH assembly, NM1 mediates physical recruitment of the histone acetyl transferase PCAF and the histone methyl transferase Set1/Ash2 to maintain and preserve H3K9acetylation and H3K4trimethylation for active transcription. Conclusions We propose a novel genome-wide mechanism where myosin synergizes with Pol II-associated actin to link the polymerase machinery with permissive chromatin for transcription activation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0147-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
| | - Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden. .,Present address: National Institute of Health, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20892-3675, USA.
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
| |
Collapse
|
15
|
Sarshad AA, Corcoran M, Al-Muzzaini B, Borgonovo-Brandter L, Von Euler A, Lamont D, Visa N, Percipalle P. Glycogen synthase kinase (GSK) 3β phosphorylates and protects nuclear myosin 1c from proteasome-mediated degradation to activate rDNA transcription in early G1 cells. PLoS Genet 2014; 10:e1004390. [PMID: 24901984 PMCID: PMC4046919 DOI: 10.1371/journal.pgen.1004390] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/03/2014] [Indexed: 11/17/2022] Open
Abstract
Nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by facilitating PCAF-mediated H3K9 acetylation, but the molecular mechanism by which NM1 is regulated remains unclear. Here, we report that at early G1 the glycogen synthase kinase (GSK) 3β phosphorylates and stabilizes NM1, allowing for NM1 association with the chromatin. Genomic analysis by ChIP-Seq showed that this mechanism occurs on the rDNA as active GSK3β selectively occupies the gene. ChIP assays and transmission electron microscopy in GSK3β−/− mouse embryonic fibroblasts indicated that at G1 rRNA synthesis is suppressed due to decreased H3K9 acetylation leading to a chromatin state incompatible with transcription. We found that GSK3β directly phosphorylates the endogenous NM1 on a single serine residue (Ser-1020) located within the NM1 C-terminus. In G1 this phosphorylation event stabilizes NM1 and prevents NM1 polyubiquitination by the E3 ligase UBR5 and proteasome-mediated degradation. We conclude that GSK3β-mediated phosphorylation of NM1 is required for pol I transcription activation. Nuclear actin and myosin are essential regulators of gene expression. At the exit of mitosis, nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by modulating assembly of the chromatin remodeling complex WICH with the subunits WSTF and SNF2h and, crucially, facilitating H3K9 acetylation by the histone acetyl transferase PCAF. The molecular mechanism by which NM1 is regulated remains however unknown. Here, we conducted a genome-wide screen and demonstrate that GSK3β is selectively coupled to the rDNA transcription unit. In embryonic fibroblasts lacking GSK3β there is a significant drop in rRNA synthesis levels and the rDNA is devoid of actin, NM1 and SNF2h. Concomitantly with a transcriptional block we reveal decreased levels of histone H3 acetylation by the histone acetyl transferase PCAF. At G1, transcriptional repression in the GSK3β knockout mouse embryonic fibroblasts, leads to NM1 ubiquitination by the E3 ligase UBR5 and proteasome-mediated degradation. We conclude that GSK3β suppresses NM1 degradation through the ubiquitin-proteasome system, facilitates NM1 association with the rDNA chromatin and transcription activation at G1. We therefore propose a novel and fundamental role for GSK3β as essential regulator of rRNA synthesis and cell cycle progression.
Collapse
Affiliation(s)
- Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Martin Corcoran
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Bader Al-Muzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Anne Von Euler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Douglas Lamont
- FingerPrints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | |
Collapse
|
16
|
Sarshad AA, Percipalle P. New Insight into Role of Myosin Motors for Activation of RNA Polymerases. International Review of Cell and Molecular Biology 2014; 311:183-230. [DOI: 10.1016/b978-0-12-800179-0.00004-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
17
|
|