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Ashour K, Sali S, Aldoukhi AH, Hall D, Mubaid S, Busque S, Lian XJ, Gagné JP, Khattak S, Di Marco S, Poirier GG, Gallouzi IE. pADP-ribosylation regulates the cytoplasmic localization, cleavage, and pro-apoptotic function of HuR. Life Sci Alliance 2024; 7:e202302316. [PMID: 38538092 PMCID: PMC10972696 DOI: 10.26508/lsa.202302316] [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: 08/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
HuR (ElavL1) is one of the main post-transcriptional regulators that determines cell fate. Although the role of HuR in apoptosis is well established, the post-translational modifications that govern this function remain elusive. In this study, we show that PARP1/2-mediated poly(ADP)-ribosylation (PARylation) is instrumental in the pro-apoptotic function of HuR. During apoptosis, a substantial reduction in HuR PARylation is observed. This results in the cytoplasmic accumulation and the cleavage of HuR, both of which are essential events for apoptosis. These effects are mediated by a pADP-ribose-binding motif within the HuR-HNS region (HuR PAR-binding site). Under normal conditions, the association of the HuR PAR-binding site with pADP-ribose is responsible for the nuclear retention of HuR. Mutations within this motif prevent the binding of HuR to its import factor TRN2, leading to its cytoplasmic accumulation and cleavage. Collectively, our findings underscore the role of PARylation in controlling the pro-apoptotic function of HuR, offering insight into the mechanism by which PARP1/2 enzymes regulate cell fate and adaptation to various assaults.
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Affiliation(s)
- Kholoud Ashour
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Faculty of Applied Medical Sciences, Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Sujitha Sali
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Ali H Aldoukhi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Derek Hall
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Souad Mubaid
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Sandrine Busque
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Xian Jin Lian
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Shahryar Khattak
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Imed-Eddine Gallouzi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
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2
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Mubaid S, Sanchez BJ, Algehani RA, Skopenkova V, Adjibade P, Hall DT, Busque S, Lian XJ, Ashour K, Tremblay AMK, Carlile G, Gagné JP, Diaz-Gaxiola A, Khattak S, Di Marco S, Thomas DY, Poirier GG, Gallouzi IE. Tankyrase-1 regulates RBP-mediated mRNA turnover to promote muscle fiber formation. Nucleic Acids Res 2024; 52:4002-4020. [PMID: 38321934 DOI: 10.1093/nar/gkae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Poly(ADP-ribosylation) (PARylation) is a post-translational modification mediated by a subset of ADP-ribosyl transferases (ARTs). Although PARylation-inhibition based therapies are considered as an avenue to combat debilitating diseases such as cancer and myopathies, the role of this modification in physiological processes such as cell differentiation remains unclear. Here, we show that Tankyrase1 (TNKS1), a PARylating ART, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration. Although all bona fide PARPs are expressed in muscle cells, experiments using siRNA-mediated knockdown or pharmacological inhibition show that TNKS1 is the enzyme responsible of catalyzing PARylation during myogenesis. Via this activity, TNKS1 controls the turnover of mRNAs encoding myogenic regulatory factors such as nucleophosmin (NPM) and myogenin. TNKS1 mediates these effects by targeting RNA-binding proteins such as Human Antigen R (HuR). HuR harbors a conserved TNKS-binding motif (TBM), the mutation of which not only prevents the association of HuR with TNKS1 and its PARylation, but also precludes HuR from regulating the turnover of NPM and myogenin mRNAs as well as from promoting myogenesis. Therefore, our data uncover a new role for TNKS1 as a key modulator of RBP-mediated post-transcriptional events required for vital processes such as myogenesis.
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Affiliation(s)
- Souad Mubaid
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Brenda Janice Sanchez
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Rinad A Algehani
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Viktoriia Skopenkova
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Pauline Adjibade
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Derek T Hall
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Sandrine Busque
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Xian Jin Lian
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Kholoud Ashour
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Anne-Marie K Tremblay
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Graeme Carlile
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Andrea Diaz-Gaxiola
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Shahryar Khattak
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - David Y Thomas
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Imed-Eddine Gallouzi
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
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3
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Huai Y, Wang X, Mao W, Wang X, Zhao Y, Chu X, Huang Q, Ru K, Zhang L, Li Y, Chen Z, Qian A. HuR-positive stress granules: Potential targets for age-related osteoporosis. Aging Cell 2024; 23:e14053. [PMID: 38375951 PMCID: PMC10928564 DOI: 10.1111/acel.14053] [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: 07/17/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 02/21/2024] Open
Abstract
Aging impairs osteoblast function and bone turnover, resulting in age-related bone degeneration. Stress granules (SGs) are membrane-less organelles that assemble in response to stress via the recruitment of RNA-binding proteins (RBPs), and have emerged as a novel mechanism in age-related diseases. Here, we identified HuR as a bone-related RBP that aggregated into SGs and facilitated osteogenesis during aging. HuR-positive SG formation increased during osteoblast differentiation, and HuR overexpression mitigated the reduction in SG formation observed in senescent osteoblasts. Moreover, HuR positively regulated the mRNA stability and expression of its target β-catenin by binding and recruiting β-catenin into SGs. As a potential therapeutic target, HuR activator apigenin (API) enhanced its expression and thus aided osteoblasts differentiation. API treatment increased HuR nuclear export, enhanced the recruitment of β-catenin into HuR-positive SGs, facilitated β-catenin nuclear translocation, and contributed osteogenesis. Our findings highlight the roles of HuR and its SGs in promoting osteogenesis during skeletal aging and lay the groundwork for novel therapeutic strategies against age-related skeletal disorders.
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Affiliation(s)
- Ying Huai
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
- Department of OrthopedicsTangdu Hospital, Air Force Military Medical UniversityXi'anChina
| | - Xue Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Wenjing Mao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Xuehao Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Yipu Zhao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Xiaohua Chu
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Qian Huang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Kang Ru
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Ling Zhang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Yu Li
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Zhihao Chen
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
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4
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Goswami B, Nag S, Ray PS. Fates and functions of RNA-binding proteins under stress. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1825. [PMID: 38014833 DOI: 10.1002/wrna.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/03/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
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5
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Jiang B, Yuan Y, Yi T, Dang W. The Roles of Antisense Long Noncoding RNAs in Tumorigenesis and Development through Cis-Regulation of Neighbouring Genes. Biomolecules 2023; 13:684. [PMID: 37189431 PMCID: PMC10135817 DOI: 10.3390/biom13040684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antisense long noncoding RNA (as-lncRNA) is a lncRNA transcribed in reverse orientation that is partially or completely complementary to the corresponding sense protein-coding or noncoding genes. As-lncRNAs, one of the natural antisense transcripts (NATs), can regulate the expression of their adjacent sense genes through a variety of mechanisms, affect the biological activities of cells, and further participate in the occurrence and development of a variety of tumours. This study explores the functional roles of as-lncRNAs, which can cis-regulate protein-coding sense genes, in tumour aetiology to understand the occurrence and development of malignant tumours in depth and provide a better theoretical basis for tumour therapy targeting lncRNAs.
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Affiliation(s)
- Binyuan Jiang
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Yeqin Yuan
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Ting Yi
- Department of Science and Education, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Wei Dang
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Department of Science and Education, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
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6
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Sun Y, Zhan S, Zhao S, Zhong T, Wang L, Guo J, Dai D, Li D, Cao J, Li L, Zhang H. HuR Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Regulating Myomaker mRNA Stability. Int J Mol Sci 2023; 24:ijms24086893. [PMID: 37108057 PMCID: PMC10138435 DOI: 10.3390/ijms24086893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Human antigen R (HuR) is an RNA-binding protein that contributes to a wide variety of biological processes and diseases. HuR has been demonstrated to regulate muscle growth and development, but its regulatory mechanisms are not well understood, especially in goats. In this study, we found that HuR was highly expressed in the skeletal muscle of goats, and its expression levels changed during longissimus dorsi muscle development in goats. The effects of HuR on goat skeletal muscle development were explored using skeletal muscle satellite cells (MuSCs) as a model. The overexpression of HuR accelerated the expression of myogenic differentiation 1 (MyoD), Myogenin (MyoG), myosin heavy chain (MyHC), and the formation of myotubes, while the knockdown of HuR showed opposite effects in MuSCs. In addition, the inhibition of HuR expression significantly reduced the mRNA stability of MyoD and MyoG. To determine the downstream genes affected by HuR at the differentiation stage, we conducted RNA-Seq using MuSCs treated with small interfering RNA, targeting HuR. The RNA-Seq screened 31 upregulated and 113 downregulated differentially expressed genes (DEGs) in which 11 DEGs related to muscle differentiation were screened for quantitative real-time PCR (qRT-PCR) detection. Compared to the control group, the expression of three DEGs (Myomaker, CHRNA1, and CAPN6) was significantly reduced in the siRNA-HuR group (p < 0.01). In this mechanism, HuR bound to Myomaker and increased the mRNA stability of Myomaker. It then positively regulated the expression of Myomaker. Moreover, the rescue experiments indicated that the overexpression of HuR may reverse the inhibitory impact of Myomaker on myoblast differentiation. Together, our findings reveal a novel role for HuR in promoting muscle differentiation in goats by increasing the stability of Myomaker mRNA.
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Affiliation(s)
- Yanjin Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Sen Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dinghui Dai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
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7
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Guha A, Husain MA, Si Y, Nabors LB, Filippova N, Promer G, Smith R, King PH. RNA regulation of inflammatory responses in glia and its potential as a therapeutic target in central nervous system disorders. Glia 2023; 71:485-508. [PMID: 36380708 DOI: 10.1002/glia.24288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022]
Abstract
A major hallmark of neuroinflammation is the activation of microglia and astrocytes with the induction of inflammatory mediators such as IL-1β, TNF-α, iNOS, and IL-6. Neuroinflammation contributes to disease progression in a plethora of neurological disorders ranging from acute CNS trauma to chronic neurodegenerative disease. Posttranscriptional pathways of mRNA stability and translational efficiency are major drivers for the expression of these inflammatory mediators. A common element in this level of regulation centers around the adenine- and uridine-rich element (ARE) which is present in the 3' untranslated region (UTR) of the mRNAs encoding these inflammatory mediators. (ARE)-binding proteins (AUBPs) such as Human antigen R (HuR), Tristetraprolin (TTP) and KH- type splicing regulatory protein (KSRP) are key nodes for directing these posttranscriptional pathways and either promote (HuR) or suppress (TTP and KSRP) glial production of inflammatory mediators. This review will discuss basic concepts of ARE-mediated RNA regulation and its impact on glial-driven neuroinflammatory diseases. We will discuss strategies to target this novel level of gene regulation for therapeutic effect and review exciting preliminary studies that underscore its potential for treating neurological disorders.
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Affiliation(s)
- Abhishek Guha
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mohammed Amir Husain
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ying Si
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - L Burt Nabors
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Natalia Filippova
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Grace Promer
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Reed Smith
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter H King
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Birmingham Department of Veterans Health Care System, Birmingham, Alabama, USA.,Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, USA
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8
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Sánchez BJ, Mubaid S, Busque S, de los Santos Y, Ashour K, Sadek J, Lian X, Khattak S, Di Marco S, Gallouzi IE. The formation of HuR/YB1 complex is required for the stabilization of target mRNA to promote myogenesis. Nucleic Acids Res 2023; 51:1375-1392. [PMID: 36629268 PMCID: PMC9943665 DOI: 10.1093/nar/gkac1245] [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: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
mRNA stability is the mechanism by which cells protect transcripts allowing their expression to execute various functions that affect cell metabolism and fate. It is well-established that RNA binding proteins (RBPs) such as HuR use their ability to stabilize mRNA targets to modulate vital processes such as muscle fiber formation (myogenesis). However, the machinery and the mechanisms regulating mRNA stabilization are still elusive. Here, we identified Y-Box binding protein 1 (YB1) as an indispensable HuR binding partner for mRNA stabilization and promotion of myogenesis. Both HuR and YB1 bind to 409 common mRNA targets, 147 of which contain a U-rich consensus motif in their 3' untranslated region (3'UTR) that can also be found in mRNA targets in other cell systems. YB1 and HuR form a heterodimer that associates with the U-rich consensus motif to stabilize key promyogenic mRNAs. The formation of this complex involves a small domain in HuR (227-234) that if mutated prevents HuR from reestablishing myogenesis in siHuR-treated muscle cells. Together our data uncover that YB1 is a key player in HuR-mediated stabilization of pro-myogenic mRNAs and provide the first indication that the mRNA stability mechanism is as complex as other key cellular processes such as mRNA decay and translation.
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Affiliation(s)
- Brenda Janice Sánchez
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia,KAUST Biological Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia,Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Souad Mubaid
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Sandrine Busque
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Yossef Lopez de los Santos
- KAUST Biological Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Kholoud Ashour
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Jason Sadek
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Xian Jin Lian
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
| | - Shahryar Khattak
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia,KAUST Biological Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia,KAUST Biological Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia,Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G1Y6, Canada,Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A1A3, Canada
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9
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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10
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Yang W, Yang L, Wang J, Zhang Y, Li S, Yin Q, Suo J, Ma R, Ye Y, Cheng H, Li J, Hui J, Hu P. Msi2-mediated MiR7a-1 processing repression promotes myogenesis. J Cachexia Sarcopenia Muscle 2022; 13:728-742. [PMID: 34877814 PMCID: PMC8818652 DOI: 10.1002/jcsm.12882] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 10/02/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Most of the microRNAs (MiRs) involved in myogenesis are transcriptional regulated. The role of MiR biogenesis in myogenesis has not been characterized yet. RNA-binding protein Musashi 2 (Msi2) is considered to be one of the major drivers for oncogenesis and stem cell proliferation. The functions of Msi2 in myogenesis have not been explored yet. We sought to investigate Msi2-regulated biogenesis of MiRs in myogenesis and muscle stem cell (MuSC) ageing. METHODS We detected the expression of Msi2 in MuSCs and differentiated myotubes by quantitative reverse transcription PCR (RT-qPCR) and western blot. Msi2-binding partner human antigen R (HuR) was identified by immunoprecipitation followed by mass spectrometry analysis. The cooperative binding of Msi2 and HuR on MiR7a-1 was analysed by RNA immunoprecipitation and electrophoresis mobility shift assays. The inhibition of the processing of pri-MiR7a-1 mediated by Msi2 and HuR was shown by Msi2 and HuR knockdown. Immunofluorescent staining, RT-qPCR and immunoblotting were used to characterize the function of MiR7a-1 in myogenesis. Msi2 and HuR up-regulate cryptochrome circadian regulator 2 (Cry2) via MiR7a-1 was confirmed by the luciferase assay and western blot. The post-transcriptional regulatory cascade was further confirmed by RNAi and overexpressing of Msi2 and HuR in MuSCs, and the in vivo function was characterized by histopathological and molecular biological methods in Msi2 knockout mice. RESULTS We identified a post-transcription regulatory cascade governed by a pair of RNA-binding proteins Msi2 and HuR. Msi2 is enriched in differentiated muscle cells and promotes MuSC differentiation despite its pro-proliferation functions in other cell types. Msi2 works synergistically with another RNA-binding protein HuR to repress the biogenesis of MiR7a-1 in an Msi2 dose-dependent manner to regulate the translation of the key component of the circadian core oscillator complex Cry2. Down-regulation of Cry2 (0.6-fold, vs. control, P < 0.05) mediated by MiR7a-1 represses MuSC differentiation. The disruption of this cascade leads to differentiation defects of MuSCs. In aged muscles, Msi2 (0.3-fold, vs. control, P < 0.01) expression declined, and the Cry2 protein level also decreases (0.5-fold, vs. control, P < 0.05), suggesting that the disruption of the Msi2-mediated post-transcriptional regulatory cascade could attribute to the declined ability of muscle regeneration in aged skeletal muscle. CONCLUSIONS Our findings have identified a new post-transcriptional cascade regulating myogenesis. The cascade is disrupted in skeletal muscle ageing, which leads to declined muscle regeneration ability.
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Affiliation(s)
- Wenjun Yang
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Lele Yang
- Guangzhou Laboratory, Guangzhou, China.,Max Planck Center for Tissue Stem Cells and Regenerative Medicine, Bioland Laboratory, Guangzhou, China
| | - Jianhua Wang
- Department of Orthopaedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yuanyuan Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Sheng Li
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qi Yin
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jinlong Suo
- Department of Orthopedic Surgery and Institute of Microsurgery on Extremities, Shanghai Jiaotong University Affiliated Sixth 's Hospital, Shanghai, China
| | - Ruimiao Ma
- Guangzhou Laboratory, Guangzhou, China.,Max Planck Center for Tissue Stem Cells and Regenerative Medicine, Bioland Laboratory, Guangzhou, China
| | - Yuzhen Ye
- Guangzhou Laboratory, Guangzhou, China.,Max Planck Center for Tissue Stem Cells and Regenerative Medicine, Bioland Laboratory, Guangzhou, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- Shanghai Key Laboratory of Molecular Andrology, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Ping Hu
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Guangzhou Laboratory, Guangzhou, China.,Max Planck Center for Tissue Stem Cells and Regenerative Medicine, Bioland Laboratory, Guangzhou, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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11
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Chellappan R, Guha A, Si Y, Kwan T, Nabors LB, Filippova N, Yang X, Myneni AS, Meesala S, Harms AS, King PH. SRI-42127, a novel small molecule inhibitor of the RNA regulator HuR, potently attenuates glial activation in a model of lipopolysaccharide-induced neuroinflammation. Glia 2022; 70:155-172. [PMID: 34533864 PMCID: PMC8595840 DOI: 10.1002/glia.24094] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 01/03/2023]
Abstract
Glial activation with the production of pro-inflammatory mediators is a major driver of disease progression in neurological processes ranging from acute traumatic injury to chronic neurodegenerative diseases such as amyotrophic lateral sclerosis and Alzheimer's disease. Posttranscriptional regulation is a major gateway for glial activation as many mRNAs encoding pro-inflammatory mediators contain adenine- and uridine-rich elements (ARE) in the 3' untranslated region which govern their expression. We have previously shown that HuR, an RNA regulator that binds to AREs, plays a major positive role in regulating inflammatory cytokine production in glia. HuR is predominantly nuclear in localization but translocates to the cytoplasm to exert a positive regulatory effect on RNA stability and translational efficiency. Homodimerization of HuR is necessary for translocation and we have developed a small molecule inhibitor, SRI-42127, that blocks this process. Here we show that SRI-42127 suppressed HuR translocation in LPS-activated glia in vitro and in vivo and significantly attenuated the production of pro-inflammatory mediators including IL1β, IL-6, TNF-α, iNOS, CXCL1, and CCL2. Cytokines typically associated with anti-inflammatory effects including TGF-β1, IL-10, YM1, and Arg1 were either unaffected or minimally affected. SRI-42127 suppressed microglial activation in vivo and attenuated the recruitment/chemotaxis of neutrophils and monocytes. RNA kinetic studies and luciferase studies indicated that SRI-42127 has inhibitory effects both on mRNA stability and gene promoter activation. In summary, our findings underscore HuR's critical role in promoting glial activation and the potential for SRI-42127 and other HuR inhibitors for treating neurological diseases driven by this activation.
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Affiliation(s)
- Rajeshwari Chellappan
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294,,Birmingham Veterans Affairs Medical Center, Birmingham, AL 35294
| | - Abhishek Guha
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ying Si
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294,,Birmingham Veterans Affairs Medical Center, Birmingham, AL 35294
| | - Thaddaeus Kwan
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - L. Burt Nabors
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Natalia Filippova
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Xiuhua Yang
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Anish S. Myneni
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Shriya Meesala
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ashley S Harms
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Peter H. King
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294,,Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294,,Birmingham Veterans Affairs Medical Center, Birmingham, AL 35294,Correspondence to: Dr. P.H. King; UAB Dept. of Neurology, Civitan 545C, 1530 3 Avenue South, Birmingham, AL 35294-0017, USA. Tel. (205) 975-8116; Fax (205) 996-7255;
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12
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Trivlidis J, Aloufi N, Al-Habeeb F, Nair P, Azuelos I, Eidelman DH, Baglole CJ. HuR drives lung fibroblast differentiation but not metabolic reprogramming in response to TGF-β and hypoxia. Respir Res 2021; 22:323. [PMID: 34963461 PMCID: PMC8715577 DOI: 10.1186/s12931-021-01916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Pulmonary fibrosis is thought to be driven by recurrent alveolar epithelial injury which leads to the differentiation of fibroblasts into α-smooth muscle actin (α-SMA)-expressing myofibroblasts and subsequent deposition of extracellular matrix (ECM). Transforming growth factor beta-1 (TGF-β1) plays a key role in fibroblast differentiation, which we have recently shown involves human antigen R (HuR). HuR is an RNA binding protein that also increases the translation of hypoxia inducible factor (HIF-1α) mRNA, a transcription factor critical for inducing a metabolic shift from oxidative phosphorylation towards glycolysis. This metabolic shift may cause fibroblast differentiation. We hypothesized that under hypoxic conditions, HuR controls myofibroblast differentiation and glycolytic reprogramming in human lung fibroblasts (HLFs). Methods Primary HLFs were cultured in the presence (or absence) of TGF-β1 (5 ng/ml) under hypoxic (1% O2) or normoxic (21% O2) conditions. Evaluation included mRNA and protein expression of glycolytic and myofibroblast/ECM markers by qRT-PCR and western blot. Metabolic profiling was done by proton nuclear magnetic resonance (1H- NMR). Separate experiments were conducted to evaluate the effect of HuR on metabolic reprogramming using siRNA-mediated knock-down. Results Hypoxia alone had no significant effect on fibroblast differentiation or metabolic reprogramming. While hypoxia- together with TGFβ1- increased mRNA levels of differentiation and glycolysis genes, such as ACTA2, LDHA, and HK2, protein levels of α-SMA and collagen 1 were significantly reduced. Hypoxia induced cytoplasmic translocation of HuR. Knockdown of HuR reduced features of fibroblast differentiation in response to TGF-β1 with and without hypoxia, including α-SMA and the ECM marker collagen I, but had no effect on lactate secretion. Conclusions Hypoxia reduced myofibroblasts differentiation and lactate secretion in conjunction with TGF-β. HuR is an important protein in the regulation of myofibroblast differentiation but does not control glycolysis in HLFs in response to hypoxia. More research is needed to understand the functional implications of HuR in IPF pathogenesis.
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13
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Shi DL, Grifone R. RNA-Binding Proteins in the Post-transcriptional Control of Skeletal Muscle Development, Regeneration and Disease. Front Cell Dev Biol 2021; 9:738978. [PMID: 34616743 PMCID: PMC8488162 DOI: 10.3389/fcell.2021.738978] [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: 07/09/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
Embryonic myogenesis is a temporally and spatially regulated process that generates skeletal muscle of the trunk and limbs. During this process, mononucleated myoblasts derived from myogenic progenitor cells within the somites undergo proliferation, migration and differentiation to elongate and fuse into multinucleated functional myofibers. Skeletal muscle is the most abundant tissue of the body and has the remarkable ability to self-repair by re-activating the myogenic program in muscle stem cells, known as satellite cells. Post-transcriptional regulation of gene expression mediated by RNA-binding proteins is critically required for muscle development during embryogenesis and for muscle homeostasis in the adult. Differential subcellular localization and activity of RNA-binding proteins orchestrates target gene expression at multiple levels to regulate different steps of myogenesis. Dysfunctions of these post-transcriptional regulators impair muscle development and homeostasis, but also cause defects in motor neurons or the neuromuscular junction, resulting in muscle degeneration and neuromuscular disease. Many RNA-binding proteins, such as members of the muscle blind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) families, display both overlapping and distinct targets in muscle cells. Thus they function either cooperatively or antagonistically to coordinate myoblast proliferation and differentiation. Evidence is accumulating that the dynamic interplay of their regulatory activity may control the progression of myogenic program as well as stem cell quiescence and activation. Moreover, the role of RNA-binding proteins that regulate post-transcriptional modification in the myogenic program is far less understood as compared with transcription factors involved in myogenic specification and differentiation. Here we review past achievements and recent advances in understanding the functions of RNA-binding proteins during skeletal muscle development, regeneration and disease, with the aim to identify the fundamental questions that are still open for further investigations.
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Affiliation(s)
- De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
| | - Raphaëlle Grifone
- Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
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14
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Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun 2021; 12:5605. [PMID: 34556645 PMCID: PMC8460807 DOI: 10.1038/s41467-021-25763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.
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Affiliation(s)
- Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Michael Ante
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, 1030, Vienna, Austria
| | - Cu Nguyen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Dalia Daujotyte
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Neelam Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Qingrong Chen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Chunhua Yan
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19017, US
| | - Daoud Meerzaman
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US.
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15
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Grifone R, Saquet A, Desgres M, Sangiorgi C, Gargano C, Li Z, Coletti D, Shi DL. Rbm24 displays dynamic functions required for myogenic differentiation during muscle regeneration. Sci Rep 2021; 11:9423. [PMID: 33941806 PMCID: PMC8093301 DOI: 10.1038/s41598-021-88563-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle has a remarkable capacity of regeneration after injury, but the regulatory network underlying this repair process remains elusive. RNA-binding proteins play key roles in the post-transcriptional regulation of gene expression and the maintenance of tissue homeostasis and plasticity. Rbm24 regulates myogenic differentiation during early development, but its implication in adult muscle is poorly understood. Here we show that it exerts multiple functions in muscle regeneration. Consistent with its dynamic subcellular localization during embryonic muscle development, Rbm24 also displays cytoplasm to nucleus translocation during C2C12 myoblast differentiation. In adult mice, Rbm24 mRNA is enriched in slow-twitch muscles along with myogenin mRNA. The protein displays nuclear localization in both slow and fast myofibers. Upon injury, Rbm24 is rapidly upregulated in regenerating myofibers and accumulates in the myonucleus of nascent myofibers. Through satellite cell transplantation, we demonstrate that Rbm24 functions sequentially to regulate myogenic differentiation and muscle regeneration. It is required for myogenin expression at early stages of muscle injury and for muscle-specific pre-mRNA alternative splicing at late stages of regeneration. These results identify Rbm24 as a multifaceted regulator of myoblast differentiation. They provide insights into the molecular pathway orchestrating the expression of myogenic factors and muscle functional proteins during regeneration.
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Affiliation(s)
- Raphaëlle Grifone
- Laboratory of Developmental Biology (LBD), CNRS UMR7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France.
| | - Audrey Saquet
- Laboratory of Developmental Biology (LBD), CNRS UMR7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France
| | - Manon Desgres
- Laboratory of Developmental Biology (LBD), CNRS UMR7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France
| | - Claudia Sangiorgi
- Biological Adaptation and Ageing (B2A), CNRS UMR8256 and INSERM U1164, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France
| | - Caterina Gargano
- Biological Adaptation and Ageing (B2A), CNRS UMR8256 and INSERM U1164, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France
| | - Zhenlin Li
- Biological Adaptation and Ageing (B2A), CNRS UMR8256 and INSERM U1164, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France
| | - Dario Coletti
- Biological Adaptation and Ageing (B2A), CNRS UMR8256 and INSERM U1164, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France.,Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Histology and Medical Embryology Section, Sapienza University of Rome, 00161, Rome, Italy
| | - De-Li Shi
- Laboratory of Developmental Biology (LBD), CNRS UMR7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 75005, Paris, France.
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16
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Al-Habeeb F, Aloufi N, Traboulsi H, Liu X, Nair P, Haston C, Azuelos I, Huang SK, White ES, Gallouzi IE, Di Marco S, Eidelman DH, Baglole CJ. Human antigen R promotes lung fibroblast differentiation to myofibroblasts and increases extracellular matrix production. J Cell Physiol 2021; 236:6836-6851. [PMID: 33855709 DOI: 10.1002/jcp.30380] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 01/12/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a disease of progressive scarring caused by excessive extracellular matrix (ECM) deposition and activation of α-SMA-expressing myofibroblasts. Human antigen R (HuR) is an RNA binding protein that promotes protein translation. Upon translocation from the nucleus to the cytoplasm, HuR functions to stabilize messenger RNA (mRNA) to increase protein levels. However, the role of HuR in promoting ECM production, myofibroblast differentiation, and lung fibrosis is unknown. Human lung fibroblasts (HLFs) treated with transforming growth factor β1 (TGF-β1) showed a significant increase in translocation of HuR from the nucleus to the cytoplasm. TGF-β-treated HLFs that were transfected with HuR small interfering RNA had a significant reduction in α-SMA protein as well as the ECM proteins COL1A1, COL3A, and FN1. HuR was also bound to mRNA for ACTA2, COL1A1, COL3A1, and FN. HuR knockdown affected the mRNA stability of ACTA2 but not that of the ECM genes COL1A1, COL3A1, or FN. In mouse models of pulmonary fibrosis, there was higher cytoplasmic HuR in lung structural cells compared to control mice. In human IPF lungs, there was also more cytoplasmic HuR. This study is the first to show that HuR in lung fibroblasts controls their differentiation to myofibroblasts and consequent ECM production. Further research on HuR could assist in establishing the basis for the development of new target therapy for fibrotic diseases, such as IPF.
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Affiliation(s)
- Fatmah Al-Habeeb
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Noof Aloufi
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Departments of Pathology, McGill University, Montreal, Quebec, Canada
| | - Hussein Traboulsi
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xingxing Liu
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Parameswaran Nair
- Department of Medicine, McMaster University & St Joseph's Healthcare, Hamilton, Ontario, Canada
| | - Christina Haston
- Department of Computer Science, Mathematics, Physics and Statistics, University of British Columbia, British Columbia, Canada
| | - Ilan Azuelos
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Steven K Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric S White
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Imed E Gallouzi
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Faculty of Medicine, Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Sergio Di Marco
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Faculty of Medicine, Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - David H Eidelman
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Carolyn J Baglole
- Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada.,Departments of Pathology, McGill University, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
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17
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Song XH, Liao XY, Zheng XY, Liu JQ, Zhang ZW, Zhang LN, Yan YB. Human Ccr4 and Caf1 Deadenylases Regulate Proliferation and Tumorigenicity of Human Gastric Cancer Cells via Modulating Cell Cycle Progression. Cancers (Basel) 2021; 13:cancers13040834. [PMID: 33671234 PMCID: PMC7922635 DOI: 10.3390/cancers13040834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cancer cells generally reprogram their gene expression profiles to satisfy continuous growth, proliferation, and metastasis. Most eukaryotic mRNAs are degraded in a deadenylation-dependent pathway, in which deadenylases are the key enzymes. We found that human Ccr4 (hCcr4a/b) and Caf1 (hCaf1a/b), the dominant cytosolic deadenylases, were dysregulated in several types of cancers including stomach adenocarcinoma. Stably knocking down hCaf1a/b or hCcr4a/b blocks cell cycle progression by enhancing the levels of cell cycle inhibitors and by inhibiting the formation of processing bodies, which are cytosolic foci involved in mRNA metabolism. More importantly, depletion of hCaf1a/b or hCcr4a/b dramatically inhibits cell proliferation and tumorigenicity. Our results suggest that perturbating global RNA metabolism may provide a potential novel strategy for cancer treatment. Abstract Cancer cells generally have reprogrammed gene expression profiles to meet the requirements of survival, continuous division, and metastasis. An interesting question is whether the cancer cells will be affected by interfering their global RNA metabolism. In this research, we found that human Ccr4a/b (hCcr4a/b) and Caf1a/b (hCaf1a/b) deadenylases, the catalytic components of the Ccr4-Not complex, were dysregulated in several types of cancers including stomach adenocarcinoma. The impacts of the four deadenylases on cancer cell growth were studied by the establishment of four stable MKN28 cell lines with the knockdown of hCcr4a/b or hCaf1a/b or transient knockdown in several cell lines. Depletion of hCcr4a/b or hCaf1a/b significantly inhibited cell proliferation and tumorigenicity. Mechanistic studies indicated that the cells were arrested at the G2/M phase by knocking down hCaf1a, while arrested at the G0/G1 phase by depleting hCaf1b or hCcr4a/b. The four enzymes did not affect the levels of CDKs and cyclins but modulated the levels of CDK–cyclin inhibitors. We identified that hCcr4a/b, but not hCaf1a/b, targeted the p21 mRNA in the MKN28 cells. Furthermore, depletion of any one of the four deadenylases dramatically impaired processing-body formation in the MKN28 and HEK-293T cells. Our results highlight that perturbating global RNA metabolism may severely affect cancer cell proliferation, which provides a potential novel strategy for cancer treatment.
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Affiliation(s)
- Xiao-Hui Song
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xiao-Yan Liao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xu-Ying Zheng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Jia-Qian Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Zhe-Wei Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Li-Na Zhang
- College of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
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18
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Kota SK, Lim ZW, Kota SB. Elavl1 Impacts Osteogenic Differentiation and mRNA Levels of Genes Involved in ECM Organization. Front Cell Dev Biol 2021; 9:606971. [PMID: 33614643 PMCID: PMC7889968 DOI: 10.3389/fcell.2021.606971] [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: 09/16/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022] Open
Abstract
Posttranscriptional gene regulation by Adenylate Uridylate (AU) rich element RNA binding protein, Elavl1 has been implicated in embryonic development as well as progenitor cell differentiation. Elavl1 binds to hundreds of cellular messenger RNAs predominantly through interactions with AU-rich elements (AREs) found in the untranslated regions (UTRs) and functions by regulating their stability. Biological functions of Elavl1 during osteogenic differentiation of bone marrow derived mesenchymal stem cells is not well-understood. Here we report that specific knockdown of nuclear localized Elavl1 by RNA interference in multipotent BMSCs led to increased osteogenic differentiation. Differential gene expression analysis following unbiased total RNA sequencing upon Elavl1 depletion during osteogenic differentiation of BMSCs showed increased levels of multiple mRNAs that are involved in extracellular matrix organization. We further show that many of these mRNAs contain Elavl1 binding consensus motifs that are preserved in their 3′ UTRs. RNA stability analyses indicated that depletion of Elavl1 prolongs the steady state RNA levels of several of these mRNAs. Together, our data points to Elavl1 mediated negative regulation of multiple genes involved in ECM organization that play a functional role in MSC osteogenic differentiation.
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Affiliation(s)
- Satya K Kota
- Division of Bone and Mineral Research, Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Harvard University, Boston, MA, United States
| | - Zhu Wei Lim
- Division of Bone and Mineral Research, Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Harvard University, Boston, MA, United States
| | - Savithri B Kota
- Division of Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
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19
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Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA 2021; 7:ncrna7010003. [PMID: 33466464 PMCID: PMC7839045 DOI: 10.3390/ncrna7010003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.
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Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-94-601-32-09
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20
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Regulation of Fetal Genes by Transitions among RNA-Binding Proteins during Liver Development. Int J Mol Sci 2020; 21:ijms21239319. [PMID: 33297405 PMCID: PMC7731027 DOI: 10.3390/ijms21239319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
Transcripts of alpha-fetoprotein (Afp), H19, and insulin-like growth factor 2 (Igf2) genes are highly expressed in mouse fetal liver, but decrease drastically during maturation. While transcriptional regulation of these genes has been well studied, the post-transcriptional regulation of their developmental decrease is poorly understood. Here, we show that shortening of poly(A) tails and subsequent RNA decay are largely responsible for the postnatal decrease of Afp, H19, and Igf2 transcripts in mouse liver. IGF2 mRNA binding protein 1 (IMP1), which regulates stability and translation efficiency of target mRNAs, binds to these fetal liver transcripts. When IMP1 is exogenously expressed in mouse adult liver, fetal liver transcripts show higher expression and possess longer poly(A) tails, suggesting that IMP1 stabilizes them. IMP1 declines concomitantly with fetal liver transcripts as liver matures. Instead, RNA-binding proteins (RBPs) that promote RNA decay, such as cold shock domain containing protein E1 (CSDE1), K-homology domain splicing regulatory protein (KSRP), and CUG-BP1 and ETR3-like factors 1 (CELF1), bind to 3' regions of fetal liver transcripts. These data suggest that transitions among RBPs associated with fetal liver transcripts shift regulation from stabilization to decay, leading to a postnatal decrease in those fetal transcripts.
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21
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Lv W, Jin J, Xu Z, Luo H, Guo Y, Wang X, Wang S, Zhang J, Zuo H, Bai W, Peng Y, Tang J, Zhao S, Zuo B. lncMGPF is a novel positive regulator of muscle growth and regeneration. J Cachexia Sarcopenia Muscle 2020; 11:1723-1746. [PMID: 32954689 PMCID: PMC7749533 DOI: 10.1002/jcsm.12623] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 07/24/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical regulatory roles in diverse biological processes and diseases. While a large number of lncRNAs have been identified in skeletal muscles until now, their function and underlying mechanisms in skeletal myogenesis remain largely unclear. METHODS We characterized a novel functional lncRNA designated lncMGPF (lncRNA muscle growth promoting factor) using RACE, Northern blot, fluorescence in situ hybridization and quantitative real-time PCR. Its function was determined by gene overexpression, interference, and knockout experiments in C2C12 myoblasts, myogenic progenitor cells, and an animal model. The molecular mechanism by which lncMGPF regulates muscle differentiation was mainly examined by cotransfection experiments, luciferase reporter assay, RNA immunoprecipitation, RNA pull-down, and RNA stability analyses. RESULTS We report that lncMGPF, which is highly expressed in muscles and positively regulated by myoblast determination factor (MyoD), promotes myogenic differentiation of muscle cells in vivo and in vitro. lncMGPF knockout in mice substantially decreases growth rate, reduces muscle mass, and impairs muscle regeneration. Overexpression of lncMGPF in muscles can rescue the muscle phenotype of knockout mice and promote muscle growth of wild-type mice. Mechanistically, lncMGPF promotes muscle differentiation by acting as a molecular sponge of miR-135a-5p and thus increasing the expression of myocyte enhancer factor 2C (MEF2C), as well as by enhancing human antigen R-mediated messenger RNA stabilization of myogenic regulatory genes such as MyoD and myogenin (MyoG). We confirm that pig lncRNA AK394747 and human lncRNA MT510647 are homologous to mouse lncMGPF, with conserved function and mechanism during myogenesis. CONCLUSIONS Our data reveal that lncMGPF is a novel positive regulator of myogenic differentiation, muscle growth and regeneration in mice, pigs, and humans.
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Affiliation(s)
- Wei Lv
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianjun Jin
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hongmei Luo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yubo Guo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Wang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Wang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiali Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Zuo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei Bai
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yaxing Peng
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
| | - Shuhong Zhao
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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22
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G3BP1 controls the senescence-associated secretome and its impact on cancer progression. Nat Commun 2020; 11:4979. [PMID: 33020468 PMCID: PMC7536198 DOI: 10.1038/s41467-020-18734-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 09/03/2020] [Indexed: 01/07/2023] Open
Abstract
Cellular senescence is a known driver of carcinogenesis and age-related diseases, yet senescence is required for various physiological processes. However, the mechanisms and factors that control the negative effects of senescence while retaining its benefits are still elusive. Here, we show that the rasGAP SH3-binding protein 1 (G3BP1) is required for the activation of the senescent-associated secretory phenotype (SASP). During senescence, G3BP1 achieves this effect by promoting the association of the cyclic GMP-AMP synthase (cGAS) with cytosolic chromatin fragments. In turn, G3BP1, through cGAS, activates the NF-κB and STAT3 pathways, promoting SASP expression and secretion. G3BP1 depletion or pharmacological inhibition impairs the cGAS-pathway preventing the expression of SASP factors without affecting cell commitment to senescence. These SASPless senescent cells impair senescence-mediated growth of cancer cells in vitro and tumor growth in vivo. Our data reveal that G3BP1 is required for SASP expression and that SASP secretion is a primary mediator of senescence-associated tumor growth. The mechanisms that control the deleterious behaviour of senescent cells is unclear. Here, the authors show that G3BP1 is required for the induction of the senescence-associated secretory phenotype (SASP), without affecting senescence, and that SASP secretion is a primary mediator of senescence-associated tumour growth.
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23
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Cao J, Cowan DB, Wang DZ. tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. Front Pharmacol 2020; 11:572941. [PMID: 33041815 PMCID: PMC7527594 DOI: 10.3389/fphar.2020.572941] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNA-derived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retro-element reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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24
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Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1621. [PMID: 32790161 DOI: 10.1002/wrna.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
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25
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Taniuchi K, Ogasawara M. KHSRP-bound small nucleolar RNAs associate with promotion of cell invasiveness and metastasis of pancreatic cancer. Oncotarget 2020; 11:131-147. [PMID: 32010427 PMCID: PMC6968780 DOI: 10.18632/oncotarget.27413] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/16/2019] [Indexed: 01/09/2023] Open
Abstract
KH-type splicing regulatory protein (KHSRP) is an RNA-binding protein implicated in a variety of cellular processes, including splicing in the nucleus and mRNA localization and degradation in the cytoplasm. The present study reports that KHSRP promotes invasiveness and metastasis of pancreatic cancer cells. KHSRP was localized in the nucleus and cell protrusions of pancreatic cancer cell lines. Suppression of KHSRP by small interfering RNA decreased the number of cell protrusions and inhibited invasiveness and metastasis of pancreatic cancer cells. KHSRP was localized in cytoplasmic RNA granules in pancreatic cancer cells, and RNA immunoprecipitation-sequencing analysis showed that the majority of enriched RNAs that immunoprecipitated with KHSRP were small nucleolar RNAs (snoRNAs). Specific KHSRP-bound snoRNAs, SNORA18 and SNORA22, associated with formation of cell protrusions. Consequently, SNORA18 and SNORA22 contributed to cell invasiveness and tumor metastasis. Our results provide insight into the link between KHSRP-bound snoRNAs and invasiveness and metastasis of pancreatic cancers. New therapies that prevent binding of KHSRP with specific snoRNAs may hold significant clinical promise.
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Affiliation(s)
- Keisuke Taniuchi
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Kochi 783-8505, Japan.,Department of Endoscopic Diagnostics and Therapeutics, Kochi Medical School, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Mitsunari Ogasawara
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Kochi 783-8505, Japan
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26
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Siang DTC, Lim YC, Kyaw AMM, Win KN, Chia SY, Degirmenci U, Hu X, Tan BC, Walet ACE, Sun L, Xu D. The RNA-binding protein HuR is a negative regulator in adipogenesis. Nat Commun 2020; 11:213. [PMID: 31924774 PMCID: PMC6954112 DOI: 10.1038/s41467-019-14001-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Human antigen R (HuR) is an essential regulator of RNA metabolism, but its function in metabolism remains unclear. This study identifies HuR as a major repressor during adipogenesis. Knockdown and overexpression of HuR in primary adipocyte culture enhances and inhibits adipogenesis in vitro, respectively. Fat-specific knockout of HuR significantly enhances adipogenic gene program in adipose tissues, accompanied by a systemic glucose intolerance and insulin resistance. HuR knockout also results in depot-specific phenotypes: it can repress myogenesis program in brown fat, enhance inflammation program in epidydimal white fat and induce browning program in inguinal white fat. Mechanistically, HuR may inhibit adipogenesis by recognizing and modulating the stability of hundreds of adipocyte transcripts including Insig1, a negative regulator during adipogenesis. Taken together, our work establishes HuR as an important posttranscriptional regulator of adipogenesis and provides insights into how RNA processing contributes to adipocyte development.
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Affiliation(s)
- Diana Teh Chee Siang
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Yen Ching Lim
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Aung Maung Maung Kyaw
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Khaing Nwe Win
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Sook Yoong Chia
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ufuk Degirmenci
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Xiang Hu
- Departments of Endocrine and Metabolic Diseases, The first Affiliated Hospital of Wenzhou Medical University, Wenzhou, , Zhejiang, 325035, China
| | - Bryan C Tan
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Arcinas Camille Esther Walet
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
| | - Dan Xu
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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27
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Depletion of HuR in murine skeletal muscle enhances exercise endurance and prevents cancer-induced muscle atrophy. Nat Commun 2019; 10:4171. [PMID: 31519904 PMCID: PMC6744452 DOI: 10.1038/s41467-019-12186-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 08/23/2019] [Indexed: 02/07/2023] Open
Abstract
The master posttranscriptional regulator HuR promotes muscle fiber formation in cultured muscle cells. However, its impact on muscle physiology and function in vivo is still unclear. Here, we show that muscle-specific HuR knockout (muHuR-KO) mice have high exercise endurance that is associated with enhanced oxygen consumption and carbon dioxide production. muHuR-KO mice exhibit a significant increase in the proportion of oxidative type I fibers in several skeletal muscles. HuR mediates these effects by collaborating with the mRNA decay factor KSRP to destabilize the PGC-1α mRNA. The type I fiber-enriched phenotype of muHuR-KO mice protects against cancer cachexia-induced muscle loss. Therefore, our study uncovers that under normal conditions HuR modulates muscle fiber type specification by promoting the formation of glycolytic type II fibers. We also provide a proof-of-principle that HuR expression can be targeted therapeutically in skeletal muscles to combat cancer-induced muscle wasting. HuR is an RNA-binding protein that regulates myotube differentiation in vitro. Here, the authors show that the muscle-specific ablation of HuR in mice leads to enhanced endurance capacity and an increase in oxidative fibres by destabilising PGC1α-mRNA, and show that the mice are protected against cancer cachexia
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28
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Mubaid S, Ma JF, Omer A, Ashour K, Lian XJ, Sanchez BJ, Robinson S, Cammas A, Dormoy-Raclet V, Di Marco S, Chittur SV, Tenenbaum SA, Gallouzi IE. HuR counteracts miR-330 to promote STAT3 translation during inflammation-induced muscle wasting. Proc Natl Acad Sci U S A 2019; 116:17261-17270. [PMID: 31405989 PMCID: PMC6717253 DOI: 10.1073/pnas.1905172116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Debilitating cancer-induced muscle wasting, a syndrome known as cachexia, is lethal. Here we report a posttranscriptional pathway involving the RNA-binding protein HuR as a key player in the onset of this syndrome. Under these conditions, HuR switches its function from a promoter of muscle fiber formation to become an inducer of muscle loss. HuR binds to the STAT3 (signal transducer and activator of transcription 3) mRNA, which encodes one of the main effectors of this condition, promoting its expression both in vitro and in vivo. While HuR does not affect the stability and the cellular movement of this transcript, HuR promotes the translation of the STAT3 mRNA by preventing miR-330 (microRNA 330)-mediated translation inhibition. To achieve this effect, HuR directly binds to a U-rich element in the STAT3 mRNA-3'untranslated region (UTR) located within the vicinity of the miR-330 seed element. Even though the binding sites of HuR and miR-330 do not overlap, the recruitment of either one of them to the STAT3-3'UTR negatively impacts the binding and the function of the other factor. Therefore, together, our data establish the competitive interplay between HuR and miR-330 as a mechanism via which muscle fibers modulate, in part, STAT3 expression to determine their fate in response to promoters of muscle wasting.
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Affiliation(s)
- Souad Mubaid
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jennifer F Ma
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Amr Omer
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kholoud Ashour
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xian J Lian
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Brenda J Sanchez
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Samantha Robinson
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
- Université Toulouse III Paul Sabatier, 31330 Toulouse, France
- Laboratoire d'Excellence "TOUCAN," 31037 Toulouse, France
| | - Virginie Dormoy-Raclet
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux Cedex, France
| | - Sergio Di Marco
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sridar V Chittur
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Scott A Tenenbaum
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Imed-Eddine Gallouzi
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada;
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29
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Phillips BL, Banerjee A, Sanchez BJ, Di Marco S, Gallouzi IE, Pavlath GK, Corbett AH. Post-transcriptional regulation of Pabpn1 by the RNA binding protein HuR. Nucleic Acids Res 2019; 46:7643-7661. [PMID: 29939290 PMCID: PMC6125628 DOI: 10.1093/nar/gky535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023] Open
Abstract
RNA processing is critical for proper spatial and temporal control of gene expression. The ubiquitous nuclear polyadenosine RNA binding protein, PABPN1, post-transcriptionally regulates multiple steps of gene expression. Mutations in the PABPN1 gene expanding an N-terminal alanine tract in the PABPN1 protein from 10 alanines to 11–18 alanines cause the muscle-specific disease oculopharyngeal muscular dystrophy (OPMD), which affects eyelid, pharynx, and proximal limb muscles. Previous work revealed that the Pabpn1 transcript is unstable, contributing to low steady-state Pabpn1 mRNA and protein levels in vivo, specifically in skeletal muscle, with even lower levels in muscles affected in OPMD. Thus, low levels of PABPN1 protein could predispose specific tissues to pathology in OPMD. However, no studies have defined the mechanisms that regulate Pabpn1 expression. Here, we define multiple cis-regulatory elements and a trans-acting factor, HuR, which regulate Pabpn1 expression specifically in mature muscle in vitro and in vivo. We exploit multiple models including C2C12 myotubes, primary muscle cells, and mice to determine that HuR decreases Pabpn1 expression. Overall, we have uncovered a mechanism in mature muscle that negatively regulates Pabpn1 expression in vitro and in vivo, which could provide insight to future studies investigating therapeutic strategies for OPMD treatment.
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Affiliation(s)
- Brittany L Phillips
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Brenda J Sanchez
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada
| | - Sergio Di Marco
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada
| | - Imed-Eddine Gallouzi
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada.,Hamad Bin Khalifa University (HBKU), Life Sciences Division, College of Sciences and Engineering, Education City, Doha, Qatar
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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30
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Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:cells8080836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
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Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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31
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Van Pelt DW, Hettinger ZR, Vanderklish PW. RNA-binding proteins: The next step in translating skeletal muscle adaptations? J Appl Physiol (1985) 2019; 127:654-660. [PMID: 31120811 DOI: 10.1152/japplphysiol.00076.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The decline of skeletal muscle mass during illness, injury, disuse, and aging is associated with poor health outcomes. Therefore, it is important to pursue a greater understanding of the mechanisms that dictate skeletal muscle adaptation. In this review, we propose that RNA-binding proteins (RBPs) comprise a critical regulatory node in the orchestration of adaptive responses in skeletal muscle. While RBPs have broadly pleiotropic molecular functions, our discussion is constrained at the outset by observations from hibernating animals, which suggest that RBP regulation of RNA stability and its impact on translational reprogramming is a key component of skeletal muscle response to anabolic and catabolic stimuli. We discuss the limited data available on the expression and functions of RBPs in adult skeletal muscle in response to disuse, aging, and exercise. A model is proposed in which dynamic changes in RBPs play a central role in muscle adaptive processes through their differential effects on mRNA stability. While limited, the currently available data suggest that understanding how adaptive (and maladaptive) changes in the expression of RBPs regulate mRNA stability in skeletal muscle could be an informative and productive research area for finding new strategies to limit atrophy and promote hypertrophy.
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Affiliation(s)
- Douglas W Van Pelt
- College of Health Sciences, Department of Rehabilitation Sciences, University of Kentucky, Lexington, Kentucky.,Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Zachary R Hettinger
- College of Health Sciences, Department of Rehabilitation Sciences, University of Kentucky, Lexington, Kentucky.,Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Peter W Vanderklish
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California
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32
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Muscle development and regeneration controlled by AUF1-mediated stage-specific degradation of fate-determining checkpoint mRNAs. Proc Natl Acad Sci U S A 2019; 116:11285-11290. [PMID: 31113881 DOI: 10.1073/pnas.1901165116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AUF1 promotes rapid decay of mRNAs containing 3' untranslated region (3'UTR) AU-rich elements (AREs). AUF1 depletion in mice accelerates muscle loss and causes limb girdle muscular dystrophy. Here, we demonstrate that the selective, targeted degradation by AUF1 of key muscle stem cell fate-determining checkpoint mRNAs regulates each stage of muscle development and regeneration by reprogramming each myogenic stage. Skeletal muscle stem (satellite) cell explants show that Auf1 transcription is activated with satellite cell activation by stem cell regulatory factor CTCF. AUF1 then targets checkpoint ARE-mRNAs for degradation, progressively reprogramming the transcriptome through each stage of myogenesis. Transition steps in myogenesis, from stem cell proliferation to differentiation to muscle fiber development, are each controlled by fate-determining checkpoint mRNAs, which, surprisingly, were found to be controlled in their expression by AUF1-targeted mRNA decay. Checkpoint mRNAs targeted by AUF1 include Twist1, decay of which promotes myoblast development; CyclinD1, decay of which blocks myoblast proliferation and initiates differentiation; and RGS5, decay of which activates Sonic Hedgehog (SHH) pathway-mediated differentiation of mature myotubes. AUF1 therefore orchestrates muscle stem cell proliferation, self-renewal, myoblast differentiation, and ultimately formation of muscle fibers through targeted, staged mRNA decay.
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33
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [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: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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34
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Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM. Proc Natl Acad Sci U S A 2019; 116:2935-2944. [PMID: 30718402 PMCID: PMC6386705 DOI: 10.1073/pnas.1808696116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HuR is a pivotal player in binding mRNAs containing AU-rich elements and regulating their stability and decay. HuR embeds three RNA recognition motifs (RRMs). The function of RRM3 is not completely understood, and the structure of the entire Hu protein family is so far unknown. Here, we provide structural and mechanistic insights into how HuR RRM3 discriminates between U-rich and AU-rich targets. RRM3 uses additional mechanisms, like multiple-register binding and homodimerization, to fine-tune its affinity for RNA. These results highlight the multifunctional role of HuR RRM3 but also the subtle adaptability of RRMs, the most abundant RNA-binding domain in eukaryotes. Since elevated HuR levels are associated with disease, our structure may help develop new therapeutic strategies. Human antigen R (HuR) is a key regulator of cellular mRNAs containing adenylate/uridylate–rich elements (AU-rich elements; AREs). These are a major class of cis elements within 3′ untranslated regions, targeting these mRNAs for rapid degradation. HuR contains three RNA recognition motifs (RRMs): a tandem RRM1 and 2, followed by a flexible linker and a C-terminal RRM3. While RRM1 and 2 are structurally characterized, little is known about RRM3. Here we present a 1.9-Å-resolution crystal structure of RRM3 bound to different ARE motifs. This structure together with biophysical methods and cell-culture assays revealed the mechanism of RRM3 ARE recognition and dimerization. While multiple RNA motifs can be bound, recognition of the canonical AUUUA pentameric motif is possible by binding to two registers. Additionally, RRM3 forms homodimers to increase its RNA binding affinity. Finally, although HuR stabilizes ARE-containing RNAs, we found that RRM3 counteracts this effect, as shown in a cell-based ARE reporter assay and by qPCR with native HuR mRNA targets containing multiple AUUUA motifs, possibly by competing with RRM12.
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35
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Pan T, Jia P, Chen N, Fang Y, Liang Y, Guo M, Ding X. Delayed Remote Ischemic Preconditioning ConfersRenoprotection against Septic Acute Kidney Injury via Exosomal miR-21. Theranostics 2019; 9:405-423. [PMID: 30809283 PMCID: PMC6376188 DOI: 10.7150/thno.29832] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Sepsis is a common and life-threatening systemic disorder, often leading to acute injury of multiple organs. Here, we show that remote ischemic preconditioning (rIPC), elicited by brief episodes of ischemia and reperfusion in femoral arteries, provides protective effects against sepsis-induced acute kidney injury (AKI). Methods: Limb rIPC was conducted on mice in vivo 24 h before the onset of cecal ligation and puncture (CLP), and serum exosomes derived from rIPC mice were infused into CLP-challenged recipients. In vitro, we extracted and identified exosomes from differentiated C2C12 cells (myotubes) subjected to hypoxia and reoxygenation (H/R) preconditioning, and the exosomes were administered to lipopolysaccharide (LPS)-treated mouse tubular epithelial cells (mTECs) or intravenously injected into CLP-challenged miR-21 knockout mice for rescue experiments. Results: Limb rIPC protected polymicrobial septic mice from multiple organ dysfunction, systemic accumulation of inflammatory cytokines and accelerated parenchymal cell apoptosis through upregulation of miR-21 in a hypoxia-inducible factor 1α (HIF-1α)-dependent manner in the ischemic limbs of mice. However, in miR-21 knockout mice or mice that received HIF-1α siRNA injection into hind limb muscles, the organ protection conferred by limb rIPC was abolished. Mechanistically, we discovered that miR-21 was transported from preischemic limbs to remote organs via serum exosomes. In kidneys, the enhanced exosomal miR-21 derived from cultured myotubes with H/R or the serum of mice treated with rIPC integrated into renal tubular epithelial cells and then targeted the downstream PDCD4/NF-κB and PTEN/AKT pathways, exerting anti-inflammatory and anti-apoptotic effects and consequently attenuating sepsis-induced renal injury both in vivo and in vitro. Conclusion: This study demonstrates a critical role for exosomal miR-21 in renoprotection conferred by limb rIPC against sepsis and suggests that rIPC and exosomes might serve as the possible therapeutic strategies for sepsis-induced kidney injury.
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36
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The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly in myogenesis. Skelet Muscle 2018; 8:37. [PMID: 30526691 PMCID: PMC6286576 DOI: 10.1186/s13395-018-0183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/22/2018] [Indexed: 01/07/2023] Open
Abstract
Background Members of the ZFP36 family of RNA-binding proteins regulate gene expression post-transcriptionally by binding to AU-rich elements in the 3’UTR of mRNA and stimulating mRNA degradation. The proteins within this family target different transcripts in different tissues. In particular, ZFP36 targets myogenic transcripts and may have a role in adult muscle stem cell quiescence. Our study examined the requirement of ZFP36L1 and ZFP36L2 in adult muscle cell fate regulation. Methods We generated single and double conditional knockout mice in which Zfp36l1 and/or Zfp36l2 were deleted in Pax7-expressing cells. Immunostained muscle sections were used to analyse resting skeletal muscle, and a cardiotoxin-induced injury model was used to determine the regenerative capacity of muscle. Results We show that ZFP36L1 and ZFP36L2 proteins are expressed in satellite cells. Mice lacking the two proteins in Pax7-expressing cells have reduced body weight and have reduced skeletal muscle mass. Furthermore, the number of satellite cells is reduced in adult skeletal muscle and the capacity of this muscle to regenerate following muscle injury is diminished. Conclusion ZFP36L1 and ZFP36L2 act redundantly in myogenesis. These findings add further intricacy to the regulation of the cell fate of Pax7-expressing cells in skeletal muscle by RNA-binding proteins. Electronic supplementary material The online version of this article (10.1186/s13395-018-0183-9) contains supplementary material, which is available to authorized users.
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37
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A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability. PLoS Genet 2018; 14:e1007802. [PMID: 30496290 PMCID: PMC6289468 DOI: 10.1371/journal.pgen.1007802] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 12/11/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression. Breast cancer is the most common cancer in women worldwide. The molecular mechanisms underlying the disease have been extensively studied, leading to dramatic improvements in diagnostic and prognostic approaches. Despite the overall improvements in survival rate, numerous cases of death by breast cancer are still reported per year, alerting us about the potential gap of knowledge in cancer molecular biology era. The emerging advances in new generation sequencing techniques have revealed that the majority of genome is transcribed into non-protein coding RNAs or ncRNAs, including thousands of long ncRNAs (lncRNAs) of unknown function. Natural antisense RNAs (NATs) constitute a group of lncRNAs that are transcribed in the opposite direction to a sense protein-coding or non-coding gene with partial or complete complementarity. In this manuscript, we investigate the role of NATs in breast cancer progression, focusing on the role of PDCD4-AS1, a NAT expressed from the established tumor suppressor PDCD4 gene locus. We observe that both PDCD4-AS1 and PDCD4 display concordant expression in breast cancer cell lines and patients. In mammary epithelial cells, PDCD4-AS1 promotes the stability of PDCD4 mRNA. PDCD4-AS1 by forming RNA duplex with PDCD4 RNA prevents the interaction between PDCD4 RNA and RNA decay factors in the nucleus.
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38
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Sun Q, Tripathi V, Yoon JH, Singh D, Hao Q, Min KW, Davila S, Zealy R, Li X, Polycarpou-Schwarz M, Lehrmann E, Zhang Y, Becker K, Freier S, Zhu Y, Diederichs S, Prasanth S, Lal A, Gorospe M, Prasanth K. MIR100 host gene-encoded lncRNAs regulate cell cycle by modulating the interaction between HuR and its target mRNAs. Nucleic Acids Res 2018; 46:10405-10416. [PMID: 30102375 PMCID: PMC6212728 DOI: 10.1093/nar/gky696] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/12/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate vital biological processes, including cell proliferation, differentiation and development. A subclass of lncRNAs is synthesized from microRNA (miRNA) host genes (MIRHGs) due to pre-miRNA processing, and are categorized as miRNA-host gene lncRNAs (lnc-miRHGs). Presently, the cellular function of most lnc-miRHGs is not well understood. We demonstrate a miRNA-independent role for a nuclear-enriched lnc-miRHG in cell cycle progression. MIR100HG produces spliced and stable lncRNAs that display elevated levels during the G1 phase of the cell cycle. Depletion of MIR100HG-encoded lncRNAs in human cells results in aberrant cell cycle progression without altering the levels of miRNA encoded within MIR100HG. Notably, MIR100HG interacts with HuR/ELAVL1 as well as with several HuR-target mRNAs. Further, MIR100HG-depleted cells show reduced interaction between HuR and three of its target mRNAs, indicating that MIR100HG facilitates interaction between HuR and target mRNAs. Our studies have unearthed novel roles played by a MIRHG-encoded lncRNA in regulating RNA binding protein activity, thereby underscoring the importance of determining the function of several hundreds of lnc-miRHGs that are present in human genome.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Vidisha Tripathi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Richard W Zealy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Maria Polycarpou-Schwarz
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | | | - Yuelin Zhu
- Molecular Genetics Section, CCR, NCI, NIH, Bethesda, MD, USA
| | - Sven Diederichs
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115, 79106 Freiburg & German Cancer Consortium (DKTK), Freiburg, Germany
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
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Kudou K, Komatsu T, Nogami J, Maehara K, Harada A, Saeki H, Oki E, Maehara Y, Ohkawa Y. The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation. Open Biol 2018; 7:rsob.170119. [PMID: 28878038 PMCID: PMC5627051 DOI: 10.1098/rsob.170119] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
Myogenic progenitor/stem cells retain their skeletal muscle differentiation potential by maintaining myogenic transcription factors such as MyoD. However, the mechanism of how MyoD expression is maintained in proliferative progenitor cells has not been elucidated. Here, we found that MyoD expression was reduced at the mRNA level by cell cycle arrest in S and G2 phases, which in turn led to the absence of skeletal muscle differentiation. The reduction of MyoD mRNA was correlated with the reduced expression of factors regulating RNA metabolism, including methyltransferase like 3 (Mettl3), which induces N6-methyladenosine (m6A) modifications of RNA. Knockdown of Mettl3 revealed that MyoD RNA was specifically downregulated and that this was caused by a decrease in processed, but not unprocessed, mRNA. Potential m6A modification sites were profiled by m6A sequencing and identified within the 5' untranslated region (UTR) of MyoD mRNA. Deletion of the 5' UTR revealed that it has a role in MyoD mRNA processing. These data showed that Mettl3 is required for MyoD mRNA expression in proliferative myoblasts.
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Affiliation(s)
- Kensuke Kudou
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuro Komatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Hiroshi Saeki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
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40
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Chowdhury TA, Koceja C, Eisa-Beygi S, Kleinstiver BP, Kumar SN, Lin CW, Li K, Prabhudesai S, Joung JK, Ramchandran R. Temporal and Spatial Post-Transcriptional Regulation of Zebrafish tie1 mRNA by Long Noncoding RNA During Brain Vascular Assembly. Arterioscler Thromb Vasc Biol 2018; 38:1562-1575. [PMID: 29724820 PMCID: PMC6023729 DOI: 10.1161/atvbaha.118.310848] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/19/2018] [Indexed: 12/14/2022]
Abstract
Supplemental Digital Content is available in the text. Objective— Tie1 (tyrosine kinase containing immunoglobulin and epidermal growth factor homology 1), an endothelial and hematopoietic cell–specific receptor tyrosine kinase, is an important regulator of angiogenesis and critical for maintaining vascular integrity. The post-transcriptional regulation of tie1 mRNA expression is not understood, but it might partly explain Tie1’s differential expression pattern in endothelium. Following up on our previous work that identified natural antisense transcripts from the tie1 locus—tie1 antisense (tie1AS), which regulates tie1 mRNA levels in zebrafish—we attempted to identify the mechanism of this regulation. Approach and Results— Through in vitro and in vivo ribonucleoprotein binding studies, we demonstrated that tie1AS long noncoding RNA interacts with an RNA binding protein—embryonic lethal and abnormal vision Drosophila-like 1 (Elavl1)—that regulates tie1 mRNA levels. When we disrupted the interaction between tie1AS and Elavl1 by using constitutively active antisense morpholino oligonucleotides or photoactivatable morpholino oligonucleotides, tie1 mRNA levels increased between 26 and 31 hours post-fertilization, particularly in the head. This increase correlated with dilation of primordial midbrain channels, smaller eyes, and reduced ventricular space. We also observed these phenotypes when we used CRISPR (clustered regularly interspaced short palindromic repeats)–mediated CRISPRi (CRISPR-mediated interference) to knock down tie1AS. Treatment of the morpholino oligonucleotide–injected embryos with a small molecule that decreased tie1 mRNA levels rescued all 3 abnormal phenotypes. Conclusions— We identified a novel mode of temporal and spatial post-transcriptional regulation of tie1 mRNA. It involves long noncoding RNA, tie1AS, and Elavl1 (an interactor of tie1AS).
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Affiliation(s)
| | - Chris Koceja
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.)
| | | | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown (B.P.K., J.K.J.).,Department of Pathology, Harvard Medical School, Boston, MA (B.P.K., J.K.J.)
| | | | - Chien-Wei Lin
- Division of Biostatistics (C.-W.L.), Developmental Vascular Biology Program, Children's Research Institute, Medical College of Wisconsin, Milwaukee
| | - Keguo Li
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.).,Obstetrics and Gynecology (T.A.C., K.L., R.R.)
| | | | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown (B.P.K., J.K.J.).,Department of Pathology, Harvard Medical School, Boston, MA (B.P.K., J.K.J.)
| | - Ramani Ramchandran
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.) .,Obstetrics and Gynecology (T.A.C., K.L., R.R.)
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41
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Vest KE, Paskavitz AL, Lee JB, Padilla-Benavides T. Dynamic changes in copper homeostasis and post-transcriptional regulation of Atp7a during myogenic differentiation. Metallomics 2018; 10:309-322. [PMID: 29333545 PMCID: PMC5824686 DOI: 10.1039/c7mt00324b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Copper (Cu) is an essential metal required for activity of a number of redox active enzymes that participate in critical cellular pathways such as metabolism and cell signaling. Because it is also a toxic metal, Cu must be tightly controlled by a series of transporters and chaperone proteins that regulate Cu homeostasis. The critical nature of Cu is highlighted by the fact that mutations in Cu homeostasis genes cause pathologic conditions such as Menkes and Wilson diseases. While Cu homeostasis in highly affected tissues like the liver and brain is well understood, no study has probed the role of Cu in development of skeletal muscle, another tissue that often shows pathology in these conditions. Here, we found an increase in whole cell Cu content during differentiation of cultured immortalized or primary myoblasts derived from mouse satellite cells. We demonstrate that Cu is required for both proliferation and differentiation of primary myoblasts. We also show that a key Cu homeostasis gene, Atp7a, undergoes dynamic changes in expression during myogenic differentiation. Alternative polyadenylation and stability of Atp7a mRNA fluctuates with differentiation stage of the myoblasts, indicating post-transcriptional regulation of Atp7a that depends on the differentiation state. This is the first report of a requirement for Cu during myogenic differentiation and provides the basis for understanding the network of Cu transport associated with myogenesis.
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Affiliation(s)
- Katherine E. Vest
- Department of Biology , Emory University , 1510 Clifton Road , Atlanta , GA 30322 , USA
| | - Amanda L. Paskavitz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , 394 Plantation St. , Worcester , MA 01605 , USA .
| | - Joseph B. Lee
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , 394 Plantation St. , Worcester , MA 01605 , USA .
| | - Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , 394 Plantation St. , Worcester , MA 01605 , USA .
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42
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Boudra R, Lagrafeuille R, Lours-Calet C, de Joussineau C, Loubeau-Legros G, Chaveroux C, Saru JP, Baron S, Morel L, Beaudoin C. mTOR transcriptionally and post-transcriptionally regulates Npm1 gene expression to contribute to enhanced proliferation in cells with Pten inactivation. Cell Cycle 2018; 15:1352-62. [PMID: 27050906 DOI: 10.1080/15384101.2016.1166319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) plays essential roles in the regulation of growth-related processes such as protein synthesis, cell sizing and metabolism in both normal and pathological growing conditions. These functions of mTOR are thought to be largely a consequence of its cytoplasmic activity in regulating translation rate, but accumulating data highlight supplementary role(s) for this serine/threonine kinase within the nucleus. Indeed, the nuclear activities of mTOR are currently associated with the control of protein biosynthetic capacity through its ability to regulate the expression of gene products involved in the control of ribosomal biogenesis and proliferation. Using primary murine embryo fibroblasts (MEFs), we observed that cells with overactive mTOR signaling displayed higher abundance for the growth-associated Npm1 protein, in what represents a novel mechanism of Npm1 gene regulation. We show that Npm1 gene expression is dependent on mTOR as demonstrated by treatment of wild-type and Pten inactivated MEFs cultured with rapamycin or by transient transfections of small interfering RNA directed against mTOR. In accordance, the mTOR kinase localizes to the Npm1 promoter gene in vivo and it enhances the activity of a human NPM1-luciferase reporter gene providing an opportunity for direct control. Interestingly, rapamycin did not dislodge mTOR from the Npm1 promoter but rather strongly destabilized the Npm1 transcript by increasing its turnover. Using a prostate-specific Pten-deleted mouse model of cancer, Npm1 mRNA levels were found up-regulated and sensitive to rapamycin. Finally, we also showed that Npm1 is required to promote mTOR-dependent cell proliferation. We therefore proposed a model whereby mTOR is closely involved in the transcriptional and posttranscriptional regulation of Npm1 gene expression with implications in development and diseases including cancer.
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Affiliation(s)
- Rafik Boudra
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Rosyne Lagrafeuille
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Corinne Lours-Calet
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Cyrille de Joussineau
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Gaëlle Loubeau-Legros
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Cédric Chaveroux
- d Inserm U1052, CNRS UMR5286, Center de Recherche en Cancérologie de Lyon , Lyon , France
| | - Jean-Paul Saru
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Silvère Baron
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Laurent Morel
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
| | - Claude Beaudoin
- a Université Clermont Auvergne, Université Blaise Pascal, GReD , BP 10448 , Clermont-Ferrand , France.,b CNRS, UMR6293, GReD , Clermont-Ferrand , France.,c Inserm, UMR1103, GReD , Clermont-Ferrand , France
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43
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Yuan H, Deng R, Zhao X, Chen R, Hou G, Zhang H, Wang Y, Xu M, Jiang B, Yu J. SUMO1 modification of KHSRP regulates tumorigenesis by preventing the TL-G-Rich miRNA biogenesis. Mol Cancer 2017; 16:157. [PMID: 29020972 PMCID: PMC5637259 DOI: 10.1186/s12943-017-0724-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/15/2017] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) are important regulators involved in diverse physiological and pathological processes including cancer. SUMO (small ubiquitin-like modifier) is a reversible protein modifier. We recently found that SUMOylation of TARBP2 and DGCR8 is involved in the regulation of the miRNA pathway. KHSRP is a single stranded nucleic acid binding protein with roles in transcription and mRNA decay, and it is also a component of the Drosha-DGCR8 complex promoting the miRNA biogenesis. Methods The in vivo SUMOylation assay using the Ni2+-NTA affinity pulldown or immunoprecipitation (IP) and the in vitro E.coli-based SUMOylation assay were used to analyze SUMOylation of KHSRP. Nuclear/Cytosol fractionation assay and immunofluorescent staining were used to observe the localization of KHSRP. High-throughput miRNA sequencing, quantantive RT-PCR and RNA immunoprecipitation assay (RIP) were employed to determine the effects of KHSRP SUMO1 modification on the miRNA biogenesis. The soft-agar colony formation, migration, vasculogenic mimicry (VM) and three-dimensional (3D) cell culture assays were performed to detect the phenotypes of tumor cells in vitro, and the xenograft tumor model in mice was conducted to verify that SUMO1 modification of KHSRP regulated tumorigenesis in vivo. Results KHSRP is modified by SUMO1 at the major site K87, and this modification can be increased upon the microenvironmental hypoxia while reduced by the treatment with growth factors. SUMO1 modification of KHSRP inhibits its interaction with the pri-miRNA/Drosha-DGCR8 complex and probably increases its translocation from the nucleus to the cytoplasm. Consequently, SUMO1 modification of KHSRP impairs the processing step of pre-miRNAs from pri-miRNAs which especially harbor short G-rich stretches in their terminal loops (TL), resulting in the downregulation of a subset of TL-G-Rich miRNAs such as let-7 family and consequential tumorigenesis. Conclusions Our data demonstrate how the miRNA biogenesis pathway is connected to tumorigenesis and cancer progression through the reversible SUMO1 modification of KHSRP. Electronic supplementary material The online version of this article (10.1186/s12943-017-0724-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haihua Yuan
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai, 201999, China.,Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rong Deng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ran Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guofang Hou
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai, 201999, China.,Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hailong Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanli Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming Xu
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai, 201999, China
| | - Bin Jiang
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai, 201999, China.
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China.
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44
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Translational Control of the Myogenic Program in Developing, Regenerating, and Diseased Skeletal Muscle. Curr Top Dev Biol 2017; 126:67-98. [PMID: 29305004 DOI: 10.1016/bs.ctdb.2017.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Translational control of genes that code for protein allows a cell to rapidly respond to changes in its environment, in part because translational control of gene expression does not depend on upstream events required to produce an mRNA molecule. The importance of translational control has been highlighted by studies concerning muscle development, regeneration, and disease. Translational control of specific mRNAs is achieved by microRNAs and RNA-binding proteins, which are particularly relevant to developmental myogenesis, where they ensure the stepwise differentiation of multipotent progenitors to committed myogenic progenitors that ultimately fuse into slow- or fast-type myofibers that make up skeletal muscle. The importance of translational control is also illustrated in muscle disease, where deregulated microRNA expression accelerates or delays progression of disease. Skeletal muscle is also unique for its remarkable capacity to regenerate after injury, which requires the activity of quiescent muscle stem cells, named satellite cells for their position underneath the basal lamina of the myofiber. Mitotically quiescent satellite cells are primed to activate the cell cycle and myogenic program, a unique feature that requires specific regulation of mRNA translation converging with pathways that regulate global protein synthesis. Emerging concepts in translational control of gene expression have shed light on multiple layers of control over the myogenic program. In parallel, the development and regeneration of skeletal muscle represents a unique, relevant, and highly defined context within which new concepts in translational control of gene expression should emerge.
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45
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Shang J, Zhao Z. Emerging role of HuR in inflammatory response in kidney diseases. Acta Biochim Biophys Sin (Shanghai) 2017; 49:753-763. [PMID: 28910975 DOI: 10.1093/abbs/gmx071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/21/2017] [Indexed: 12/14/2022] Open
Abstract
Human antigen R (HuR) is a member of the embryonic lethal abnormal vision (ELAV) family which can bind to the A/U rich elements in 3' un-translated region of mRNA and regulate mRNA splicing, transportation, and stability. Unlike other members of the ELAV family, HuR is ubiquitously expressed. Early studies mainly focused on HuR function in malignant diseases. As researches proceed, more and more proofs demonstrate its relationship with inflammation. Since most kidney diseases involve pathological changes of inflammation, HuR is now suggested to play a pivotal role in glomerular nephropathy, tubular ischemia-reperfusion damage, renal fibrosis and even renal tumors. By regulating the mRNAs of target genes, HuR is causally linked to the onset and progression of kidney diseases. Reports on this topic are steadily increasing, however, the detailed function and mechanism of action of HuR are still not well understood. The aim of this review article is to summarize the present understanding of the role of HuR in inflammation in kidney diseases, and we anticipate that future research will ultimately elucidate the therapeutic value of this novel target.
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Affiliation(s)
- Jin Shang
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhanzheng Zhao
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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46
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Anantharaman A, Tripathi V, Khan A, Yoon JH, Singh DK, Gholamalamdari O, Guang S, Ohlson J, Wahlstedt H, Öhman M, Jantsch MF, Conrad NK, Ma J, Gorospe M, Prasanth SG, Prasanth KV. ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins. Nucleic Acids Res 2017; 45:4189-4201. [PMID: 28053121 PMCID: PMC5397167 DOI: 10.1093/nar/gkw1304] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) catalyze the editing of adenosine residues to inosine (A-to-I) within RNA sequences, mostly in the introns and UTRs (un-translated regions). The significance of editing within non-coding regions of RNA is poorly understood. Here, we demonstrate that association of ADAR2 with RNA stabilizes a subset of transcripts. ADAR2 interacts with and edits the 3΄UTR of nuclear-retained Cat2 transcribed nuclear RNA (Ctn RNA). In absence of ADAR2, the abundance and half-life of Ctn RNA are significantly reduced. Furthermore, ADAR2-mediated stabilization of Ctn RNA occurred in an editing-independent manner. Unedited Ctn RNA shows enhanced interaction with the RNA-binding proteins HuR and PARN [Poly(A) specific ribonuclease deadenylase]. HuR and PARN destabilize Ctn RNA in absence of ADAR2, indicating that ADAR2 stabilizes Ctn RNA by antagonizing its degradation by PARN and HuR. Transcriptomic analysis identified other RNAs that are regulated by a similar mechanism. In summary, we identify a regulatory mechanism whereby ADAR2 enhances target RNA stability by limiting the interaction of RNA-destabilizing proteins with their cognate substrates.
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Affiliation(s)
- Aparna Anantharaman
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Vidisha Tripathi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Shuomeng Guang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Johan Ohlson
- Department of Molecular Biosciences, the WennerGren Institute, Stockholm University, SE-10691, Svante Arrheniusväg 20C, Stockholm, Sweden
| | - Helene Wahlstedt
- Department of Molecular Biosciences, the WennerGren Institute, Stockholm University, SE-10691, Svante Arrheniusväg 20C, Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, the WennerGren Institute, Stockholm University, SE-10691, Svante Arrheniusväg 20C, Stockholm, Sweden
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology and Department for Medical Biochemistry, Medical University of Vienna, A-1090, Vienna, Austria
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jian Ma
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute of Aging-Intramural Research program, NIH, Baltimore, MD 21224, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA
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Bikkavilli RK, Zerayesus SA, Van Scoyk M, Wilson L, Wu PY, Baskaran A, Tang K, Raheem S, Samuelson BA, Reddy NM, Reddy SP, Cool CD, Kosmider B, Avasarala S, Winn RA. K-homology splicing regulatory protein (KSRP) promotes post-transcriptional destabilization of Spry4 transcripts in non-small cell lung cancer. J Biol Chem 2017; 292:7423-7434. [PMID: 28275056 PMCID: PMC5418043 DOI: 10.1074/jbc.m116.757906] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/24/2017] [Indexed: 12/20/2022] Open
Abstract
AU-rich element-binding proteins (ARE-BPs) offer post-transcriptional regulation of gene expression via physical interaction and recruitment of RNA decay machinery to the AU-rich elements within the 3′-UTR of the target transcripts. However, the role of ARE-BPs in lung cancer remains poorly understood. In this study, we have identified that K-homology splicing regulatory protein (KSRP), an ARE-BP, is robustly up-regulated in human lung cancer. Importantly, Kaplan-Meier survival analysis indicated that elevated KSRP expression was correlated with poor overall survival of lung cancer patients. Furthermore, cigarette smoke, a leading risk factor for lung cancer, was also identified to be an important contributor to increased KSRP expression. Remarkably, silencing of KSRP decreased cell proliferation, reversed anchorage-independent growth, and reduced migration/invasion, suggesting an oncogenic role for KSRP in lung cancer. Finally, we provide mechanistic evidence that KSRP promotes the down-regulation of Spry4 by a previously unidentified mechanism, i.e. post-transcriptional mRNA regulation.
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Affiliation(s)
- Rama Kamesh Bikkavilli
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Sereke Adam Zerayesus
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Michelle Van Scoyk
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Lora Wilson
- Department of Pathology and Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Pei-Ying Wu
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Abhinaya Baskaran
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Ke Tang
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Syed Raheem
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Blain A Samuelson
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Narsa M Reddy
- Division of Developmental Biology and Basic Research, Department of Pediatrics,University of Illinois, Chicago, Illinois 60612
| | - Sekhar P Reddy
- Division of Developmental Biology and Basic Research, Department of Pediatrics,University of Illinois, Chicago, Illinois 60612
| | - Carlyne D Cool
- Department of Pathology and Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Beata Kosmider
- Departments of Physiology, Thoracic Medicine, and Surgery, Lewis Katz School of Medicine and.,Center for Inflammation, Translational, and Clinical Lung Research, Temple University, Philadelphia, Pennsylvania 19140.,Department of Medicine, National Jewish Health, Denver, Colorado 80206, and
| | - Sreedevi Avasarala
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and
| | - Robert A Winn
- From the Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and .,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
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Noh JH, Kim KM, Abdelmohsen K, Yoon JH, Panda AC, Munk R, Kim J, Curtis J, Moad CA, Wohler CM, Indig FE, de Paula W, Dudekula DB, De S, Piao Y, Yang X, Martindale JL, de Cabo R, Gorospe M. HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNA RMRP. Genes Dev 2016; 30:1224-39. [PMID: 27198227 PMCID: PMC4888842 DOI: 10.1101/gad.276022.115] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/14/2016] [Indexed: 01/06/2023]
Abstract
Noh et al. found two RNA-binding proteins (RBPs)—HuR and GRSF1—that associated with the nuclear DNA-encoded lncRNA RMRP and mobilized it to mitochondria. In cultured human cells, HuR bound RMRP in the nucleus and mediated its CRM1-dependent export to the cytosol. After RMRP was imported into mitochondria, GRSF1 bound RMRP and increased its abundance in the matrix. Some mitochondrial long noncoding RNAs (lncRNAs) are encoded by nuclear DNA, but the mechanisms that mediate their transport to mitochondria are poorly characterized. Using affinity RNA pull-down followed by mass spectrometry analysis, we found two RNA-binding proteins (RBPs), HuR (human antigen R) and GRSF1 (G-rich RNA sequence-binding factor 1), that associated with the nuclear DNA-encoded lncRNA RMRP and mobilized it to mitochondria. In cultured human cells, HuR bound RMRP in the nucleus and mediated its CRM1 (chromosome region maintenance 1)-dependent export to the cytosol. After RMRP was imported into mitochondria, GRSF1 bound RMRP and increased its abundance in the matrix. Loss of GRSF1 lowered the mitochondrial levels of RMRP, in turn suppressing oxygen consumption rates and modestly reducing mitochondrial DNA replication priming. Our findings indicate that RBPs HuR and GRSF1 govern the cytoplasmic and mitochondrial localization of the lncRNA RMRP, which is encoded by nuclear DNA but has key functions in mitochondria.
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Affiliation(s)
- Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Rachel Munk
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jessica Curtis
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Christopher A Moad
- Confocal Imaging Facility, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Christina M Wohler
- Confocal Imaging Facility, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Fred E Indig
- Confocal Imaging Facility, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Wilson de Paula
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Rafael de Cabo
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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49
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Essential Roles of RNA-binding Protein HuR in Activation of Hepatic Stellate Cells Induced by Transforming Growth Factor-β1. Sci Rep 2016; 6:22141. [PMID: 26912347 PMCID: PMC4766441 DOI: 10.1038/srep22141] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/08/2016] [Indexed: 11/08/2022] Open
Abstract
RNA-binding protein HuR mediates transforming growth factor (TGF)-β1-induced profibrogenic actions. Up-regulation of Sphingosine kinase 1 (SphK1) is involved in TGF-β1-induced activation of hepatic stellate cells (HSCs) in liver fibrogenesis. However, the molecular mechanism of TGF-β1 regulates SphK1 remains unclear. This study was designed to investigate the role of HuR in TGF-β1-induced SphK1 expression and identify a new molecular mechanism in liver fibrogenensis. In vivo, HuR expression was increased, translocated to cytoplasm, and bound to SphK1 mRNA in carbon tetrachloride- and bile duct ligation-induced mouse fibrotic liver. HuR mRNA expression had a positive correlation with mRNA expressions of SphK1 and fibrotic markers, α-smooth muscle actin (α-SMA) and Collagen α1(I), respectively. In vitro, up-regulation of SphK1 and activation of HSCs stimulated by TGF-β1 depended on HuR cytoplasmic accumulation. The effects of TGF-β1 were diminished when HuR was silenced or HuR cytoplasmic translocation was blocked. Meanwhile, overexpression of HuR mimicked the effects of TGF-β1. Furthermore, TGF-β1 prolonged half-life of SphK1 mRNA by promoting its binding to HuR. Pharmacological or siRNA-induced SphK1 inhibition abrogated HuR-mediated HSC activation. In conclusion, our data suggested that HuR bound to SphK1 mRNA and played a crucial role in TGF-β1-induced HSC activation.
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50
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Panda AC, Abdelmohsen K, Martindale JL, Di Germanio C, Yang X, Grammatikakis I, Noh JH, Zhang Y, Lehrmann E, Dudekula DB, De S, Becker KG, White EJ, Wilson GM, de Cabo R, Gorospe M. Novel RNA-binding activity of MYF5 enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis. Nucleic Acids Res 2016; 44:2393-408. [PMID: 26819411 PMCID: PMC4797292 DOI: 10.1093/nar/gkw023] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/08/2016] [Indexed: 01/07/2023] Open
Abstract
Skeletal muscle contains long multinucleated and contractile structures known as muscle fibers, which arise from the fusion of myoblasts into multinucleated myotubes during myogenesis. The myogenic regulatory factor (MRF) MYF5 is the earliest to be expressed during myogenesis and functions as a transcription factor in muscle progenitor cells (satellite cells) and myocytes. In mouse C2C12 myocytes, MYF5 is implicated in the initial steps of myoblast differentiation into myotubes. Here, using ribonucleoprotein immunoprecipitation (RIP) analysis, we discovered a novel function for MYF5 as an RNA-binding protein which associated with a subset of myoblast mRNAs. One prominent MYF5 target was Ccnd1 mRNA, which encodes the key cell cycle regulator CCND1 (Cyclin D1). Biotin-RNA pulldown, UV-crosslinking and gel shift experiments indicated that MYF5 was capable of binding the 3' untranslated region (UTR) and the coding region (CR) of Ccnd1 mRNA. Silencing MYF5 expression in proliferating myoblasts revealed that MYF5 promoted CCND1 translation and modestly increased transcription of Ccnd1 mRNA. Accordingly, overexpressing MYF5 in C2C12 cells upregulated CCND1 expression while silencing MYF5 reduced myoblast proliferation as well as differentiation of myoblasts into myotubes. Moreover, MYF5 silencing reduced myogenesis, while ectopically restoring CCND1 abundance partially rescued the decrease in myogenesis seen after MYF5 silencing. We propose that MYF5 enhances early myogenesis in part by coordinately elevating Ccnd1 transcription and Ccnd1 mRNA translation.
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Affiliation(s)
- Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | | | - Clara Di Germanio
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | | | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Elin Lehrmann
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Kevin G Becker
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
| | - Elizabeth J White
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD21224, USA
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