1
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Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024; 25:679-697. [PMID: 38637632 PMCID: PMC11408106 DOI: 10.1038/s41576-024-00712-2] [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] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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2
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Dubiez E, Pellegrini E, Finderup Brask M, Garland W, Foucher AE, Huard K, Heick Jensen T, Cusack S, Kadlec J. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. Cell Rep 2024; 43:113639. [PMID: 38175753 DOI: 10.1016/j.celrep.2023.113639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
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Affiliation(s)
- Etienne Dubiez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Erika Pellegrini
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maja Finderup Brask
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | | | - Karine Huard
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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3
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Kataoka N. The Nuclear Cap-Binding Complex, a multitasking binding partner of RNA polymerase II transcripts. J Biochem 2023; 175:9-15. [PMID: 37830942 PMCID: PMC10771035 DOI: 10.1093/jb/mvad081] [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: 07/24/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
In eukaryotic cells, RNAs transcribed by RNA polymerase-II receive the modification at the 5' end. This structure is called the cap structure. The cap structure has a fundamental role for translation initiation by recruiting eukaryotic translation initiation factor 4F (eIF4F). The other important mediator of the cap structure is a nuclear cap-binding protein complex (CBC). CBC consists of two proteins, which are renamed as NCBP1 and NCBP2 (previously called as CBP80/NCBP and CBP20/NIP1, respectively). This review article discusses the multiple roles CBC mediates and co-ordinates in several gene expression steps in eukaryotes.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Agriculture Bldg. 7A, Room 703, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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4
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Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
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Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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5
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Rambout X, Cho H, Blanc R, Lyu Q, Miano JM, Chakkalakal JV, Nelson GM, Yalamanchili HK, Adelman K, Maquat LE. PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII. Mol Cell 2023; 83:186-202.e11. [PMID: 36669479 PMCID: PMC9951270 DOI: 10.1016/j.molcel.2022.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/07/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023]
Abstract
PGC-1α is well established as a metazoan transcriptional coactivator of cellular adaptation in response to stress. However, the mechanisms by which PGC-1α activates gene transcription are incompletely understood. Here, we report that PGC-1α serves as a scaffold protein that physically and functionally connects the DNA-binding protein estrogen-related receptor α (ERRα), cap-binding protein 80 (CBP80), and Mediator to overcome promoter-proximal pausing of RNAPII and transcriptionally activate stress-response genes. We show that PGC-1α promotes pausing release in a two-arm mechanism (1) by recruiting the positive transcription elongation factor b (P-TEFb) and (2) by outcompeting the premature transcription termination complex Integrator. Using mice homozygous for five amino acid changes in the CBP80-binding motif (CBM) of PGC-1α that destroy CBM function, we show that efficient differentiation of primary myoblasts to myofibers and timely skeletal muscle regeneration after injury require PGC-1α binding to CBP80. Our findings reveal how PGC-1α activates stress-response gene transcription in a previously unanticipated pre-mRNA quality-control pathway.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Roméo Blanc
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Qing Lyu
- Department of Medicine, Aab Cardiovascular Research Institute, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph M Miano
- Department of Medicine, Aab Cardiovascular Research Institute, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joe V Chakkalakal
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hari K Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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6
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Cho H, Abshire ET, Popp MW, Pröschel C, Schwartz JL, Yeo GW, Maquat LE. AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay. Mol Cell 2022; 82:2779-2796.e10. [PMID: 35675814 PMCID: PMC9357146 DOI: 10.1016/j.molcel.2022.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/21/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
Abstract
Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in destroying faulty, disease-causing mRNAs and maintaining normal, physiologic mRNA abundance, additional effectors that regulate NMD activity in mammalian cells continue to be identified. Here, we describe a haploid-cell genetic screen for NMD effectors that has unexpectedly identified 13 proteins constituting the AKT signaling pathway. We show that AKT supersedes UPF2 in exon-junction complexes (EJCs) that are devoid of RNPS1 but contain CASC3, defining an unanticipated insulin-stimulated EJC. Without altering UPF1 RNA binding or ATPase activity, AKT-mediated phosphorylation of the UPF1 CH domain at T151 augments UPF1 helicase activity, which is critical for NMD and also decreases the dependence of helicase activity on ATP. We demonstrate that upregulation of AKT signaling contributes to the hyperactivation of NMD that typifies Fragile X syndrome, as exemplified using FMR1-KO neural stem cells derived from induced pluripotent stem cells.
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Affiliation(s)
- Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Elizabeth T Abshire
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Stem Cell and Regenerative Medicine Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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7
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Park J, Chang J, Hwang HJ, Jeong K, Lee HJ, Ha H, Park Y, Lim C, Woo JS, Kim YK. The pioneer round of translation ensures proper targeting of ER and mitochondrial proteins. Nucleic Acids Res 2021; 49:12517-12534. [PMID: 34850140 PMCID: PMC8643669 DOI: 10.1093/nar/gkab1098] [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: 05/02/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The pioneer (or first) round of translation of newly synthesized mRNAs is largely mediated by a nuclear cap-binding complex (CBC). In a transcriptome-wide analysis of polysome-associated and CBC-bound transcripts, we identify RN7SL1, a noncoding RNA component of a signal recognition particle (SRP), as an interaction partner of the CBC. The direct CBC–SRP interaction safeguards against abnormal expression of polypeptides from a ribosome–nascent chain complex (RNC)–SRP complex until the latter is properly delivered to the endoplasmic reticulum. Failure of this surveillance causes abnormal expression of misfolded proteins at inappropriate intracellular locations, leading to a cytosolic stress response. This surveillance pathway also blocks protein synthesis through RNC–SRP misassembled on an mRNA encoding a mitochondrial protein. Thus, our results reveal a surveillance pathway in which pioneer translation ensures proper targeting of endoplasmic reticulum and mitochondrial proteins.
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Affiliation(s)
- Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Chunghun Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae-Sung Woo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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8
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Pérez-Schindler J, Kohl B, Schneider-Heieck K, Leuchtmann AB, Henríquez-Olguín C, Adak V, Maier G, Delezie J, Sakoparnig T, Vargas-Fernández E, Karrer-Cardel B, Ritz D, Schmidt A, Hondele M, Jensen TE, Hiller S, Handschin C. RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates. Proc Natl Acad Sci U S A 2021; 118:e2105951118. [PMID: 34465622 PMCID: PMC8433555 DOI: 10.1073/pnas.2105951118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plasticity of cells, tissues, and organs is controlled by the coordinated transcription of biological programs. However, the mechanisms orchestrating such context-specific transcriptional networks mediated by the dynamic interplay of transcription factors and coregulators are poorly understood. The peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) is a prototypical master regulator of adaptive transcription in various cell types. We now uncovered a central function of the C-terminal domain of PGC-1α to bind RNAs and assemble multiprotein complexes including proteins that control gene transcription and RNA processing. These interactions are important for PGC-1α recruitment to chromatin in transcriptionally active liquid-like nuclear condensates. Notably, such a compartmentalization of active transcription mediated by liquid-liquid phase separation was observed in mouse and human skeletal muscle, revealing a mechanism by which PGC-1α regulates complex transcriptional networks. These findings provide a broad conceptual framework for context-dependent transcriptional control of phenotypic adaptations in metabolically active tissues.
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Affiliation(s)
| | - Bastian Kohl
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | - Carlos Henríquez-Olguín
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Volkan Adak
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Julien Delezie
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | | | - Danilo Ritz
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Maria Hondele
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Thomas E Jensen
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, 2100 Copenhagen, Denmark
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9
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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10
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Guha S, Bhaumik SR. Viral regulation of mRNA export with potentials for targeted therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194655. [PMID: 33246183 DOI: 10.1016/j.bbagrm.2020.194655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic gene expression begins with transcription in the nucleus to synthesize mRNA (messenger RNA), which is subsequently exported to the cytoplasm for translation to protein. Like transcription and translation, mRNA export is an important regulatory step of eukaryotic gene expression. Various factors are involved in regulating mRNA export, and thus gene expression. Intriguingly, some of these factors interact with viral proteins, and such interactions interfere with mRNA export of the host cell, favoring viral RNA export. Hence, viruses hijack host mRNA export machinery for export of their own RNAs from nucleus to cytoplasm for translation to proteins for viral life cycle, suppressing host mRNA export (and thus host gene expression and immune/antiviral response). Therefore, the molecules that can impair the interactions of these mRNA export factors with viral proteins could emerge as antiviral therapeutic agents to suppress viral RNA transport and enhance host mRNA export, thereby promoting host gene expression and immune response. Thus, there has been a number of studies to understand how virus hijacks mRNA export machinery in suppressing host gene expression and promoting its own RNA export to the cytoplasm for translation to proteins required for viral replication/assembly/life cycle towards developing targeted antiviral therapies, as concisely described here.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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11
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Zheng D, Cho H, Wang W, Rambout X, Tian B, Maquat LE. 3'READS + RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association. RNA (NEW YORK, N.Y.) 2020; 26:1621-1636. [PMID: 32796083 PMCID: PMC7566578 DOI: 10.1261/rna.076133.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Staufen1 (STAU1) is an RNA-binding protein (RBP) that interacts with double-stranded RNA structures and has been implicated in regulating different aspects of mRNA metabolism. Previous studies have indicated that STAU1 interacts extensively with RNA structures in coding regions (CDSs) and 3'-untranslated regions (3'UTRs). In particular, duplex structures formed within 3'UTRs by inverted-repeat Alu elements (IRAlus) interact with STAU1 through its double-stranded RNA-binding domains (dsRBDs). Using 3' region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3'READS + RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3'UTRs. Overall, relative to short 3'UTR counterparts, longer 3'UTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including specific IRAlus sequences. Nevertheless, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs that may recruit antagonistic RBPs and/or destabilize RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus generally have little impact on STAU1-mediated polysome association despite having strong interactions with the protein. Taken together, our work reveals complex interactions of STAU1 with its cognate RNA substrates. Our data also shed light on distinct post-transcriptional fates for the widespread APA isoforms in mammalian cells.
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Affiliation(s)
- Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Wei Wang
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action. Proc Natl Acad Sci U S A 2020; 117:22204-22213. [PMID: 32848060 DOI: 10.1073/pnas.2000643117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved in RNA regulation such as serine/arginine (SR) and RNA recognition motifs (RRMs). However, the RNA targets of PGC-1α and how they pertain to metabolism are unknown. To address this, we performed enhanced ultraviolet (UV) cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) in primary hepatocytes induced with glucagon. A large fraction of RNAs bound to PGC-1α were intronic sequences of genes involved in transcriptional, signaling, or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional PGC-1α targets such as OXPHOS or gluconeogenic genes. Among the top-scoring RNA sequences bound to PGC-1α were Foxo1, Camk1δ, Per1, Klf15, Pln4, Cluh, Trpc5, Gfra1, and Slc25a25 PGC-1α depletion decreased a fraction of these glucagon-induced messenger RNA (mRNA) transcript levels. Importantly, knockdown of several of these genes affected glucagon-dependent glucose production, a PGC-1α-regulated metabolic pathway. These studies show that PGC-1α binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action.
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13
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Rambout X, Cho H, Maquat LE. Transcriptional Coactivator PGC-1α Binding to Newly Synthesized RNA via CBP80: A Nexus for Co- and Posttranscriptional Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:47-54. [PMID: 32295928 DOI: 10.1101/sqb.2019.84.040212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mammalian cells have many quality-control mechanisms that regulate protein-coding gene expression to ensure proper transcript synthesis, processing, and translation. Should a step in transcript metabolism fail to fulfill requisite spatial, temporal, or structural criteria, including the proper acquisition of RNA-binding proteins, then that step will halt, fail to proceed to the next step, and ultimately result in transcript degradation. Quality-control mechanisms constitute a continuum of processes that initiate in the nucleus and extend to the cytoplasm. Here, we present published and unpublished data for protein-coding genes whose expression is activated by the transcriptional coactivator PGC-1α. We show that PGC-1α movement from chromatin, to which it is recruited by DNA-binding proteins, to CBP80 at the 5' cap of nascent transcripts begins a series of co- and posttranscriptional quality- and quantity-control steps that, in total, ensure proper gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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14
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Zhang H, Wang A, Tan Y, Wang S, Ma Q, Chen X, He Z. NCBP1 promotes the development of lung adenocarcinoma through up-regulation of CUL4B. J Cell Mol Med 2019; 23:6965-6977. [PMID: 31448526 PMCID: PMC6787490 DOI: 10.1111/jcmm.14581] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/06/2019] [Accepted: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
Lung cancer is the most frequent cancer type and is the leading cause of tumour‐associated deaths worldwide. Nuclear cap‐binding protein 1 (NCBP1) is necessary for capped RNA processing and intracellular localization. It has been reported that silencing of NCBP1 resulted in cell growth reduction in HeLa cells. Nevertheless, its clinical significance and underlying molecular mechanisms in non–small‐cell lung cancer remain unclear. In this study, we found that NCBP1 was significantly overexpressed in lung cancer tissues and several lung cancer cell lines. Through knockdown and overexpression experiments, we showed that NCBP1 promoted lung cancer cell growth, wound healing ability, migration and epithelial‐mesenchymal transition. Mechanistically, we found that cullin 4B (CUL4B) was a downstream target gene of NCBP1 in NSCLC. NCBP1 up‐regulated CUL4B expression via interaction with nuclear cap‐binding protein 3 (NCBP3). CUL4B silencing significantly reversed NCBP1‐induced tumorigenesis in vitro. Based on these findings, we propose a model involving the NCBP1‐NCBP3‐CUL4B oncoprotein axis, providing novel insight into how CUL4B is activated and contributes to LUAD progression.
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Affiliation(s)
- Huijun Zhang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - An Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yulong Tan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Shaohua Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Qinyun Ma
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Xiaofeng Chen
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Zelai He
- Department of Radiation Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
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15
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Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export. Mol Cell Biol 2019; 39:MCB.00540-18. [PMID: 30745412 DOI: 10.1128/mcb.00540-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
Cap-binding complex (CBC) associates cotranscriptionally with the cap structure at the 5' end of nascent mRNA to protect it from exonucleolytic degradation. Here, we show that CBC promotes the targeting of an mRNA export adaptor, Yra1 (forming transcription export [TREX] complex with THO and Sub2), to the active genes and enhances mRNA export in Saccharomyces cerevisiae Likewise, recruitment of Npl3 (an hnRNP involved in mRNA export via formation of export-competent ribonuclear protein complex [RNP]) to the active genes is facilitated by CBC. Thus, CBC enhances targeting of the export factors and promotes mRNA export. Such function of CBC is not mediated via THO and Sub2 of TREX, cleavage and polyadenylation factors, or Sus1 (that regulates mRNA export via transcription export 2 [TREX-2]). However, CBC promotes splicing of SUS1 mRNA and, consequently, Sus1 protein level and mRNA export via TREX-2. Collectively, our results support the hypothesis that CBC promotes recruitment of Yra1 and Npl3 to the active genes, independently of THO, Sub2, or cleavage and polyadenylation factors, and enhances mRNA export via TREX and RNP, respectively, in addition to its role in facilitating SUS1 mRNA splicing to increase mRNA export through TREX-2, revealing distinct stimulatory functions of CBC in mRNA export.
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16
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Miller KN, Clark JP, Anderson RM. Mitochondrial regulator PGC-1a-Modulating the modulator. ACTA ACUST UNITED AC 2019; 5:37-44. [PMID: 31406949 DOI: 10.1016/j.coemr.2019.02.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1a) is a central regulator of metabolism that is poised at the intersection of myriad intracellular signaling pathways. In this brief update, we discuss regulation of PGC-1a at multiple levels, including transcriptional, post-transcriptional, and post-translational modifications. We discuss recently identified small molecule effectors of PGC-1a that offer translational potential and promise new insight into PGC-1a biology. We highlight novel mechanistic insights relating to PGC-1a's interactions with RNA to enhance transcription and potentially influence transcript processing. Finally, we place these exciting new data in the context of aging biology, offering PGC-1a as a candidate target with terrific potential in anti-aging interventions.
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Affiliation(s)
- Karl N Miller
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Josef P Clark
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, USA.,GRECC, William S. Middleton Memorial Veterans Hospital, Madison WI, USA
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