1
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Han X, Xing L, Hong Y, Zhang X, Hao B, Lu JY, Huang M, Wang Z, Ma S, Zhan G, Li T, Hao X, Tao Y, Li G, Zhou S, Zheng Z, Shao W, Zeng Y, Ma D, Zhang W, Xie Z, Deng H, Yan J, Deng W, Shen X. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence. Cell Stem Cell 2024; 31:694-716.e11. [PMID: 38631356 DOI: 10.1016/j.stem.2024.03.015] [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: 09/22/2023] [Revised: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linqing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuechun Zhang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Hao
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - J Yuyang Lu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shaoqian Ma
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ge Zhan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowen Hao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yibing Tao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Guanwen Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuqin Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Zheng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yitian Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiangwei Yan
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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2
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Müller JM, Moos K, Baar T, Maier KC, Zumer K, Tresch A. Nuclear export is a limiting factor in eukaryotic mRNA metabolism. PLoS Comput Biol 2024; 20:e1012059. [PMID: 38753883 PMCID: PMC11135743 DOI: 10.1371/journal.pcbi.1012059] [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: 10/20/2023] [Revised: 05/29/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments of human cancer cells. We develop a model that reliably quantifies mRNA-specific synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3'UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.
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Affiliation(s)
- Jason M. Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Katharina Moos
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Till Baar
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kerstin C. Maier
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kristina Zumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne, Germany
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3
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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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4
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [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] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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5
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Chen L, Xu Z, Huang J, Shu H, Hui Y, Zhu D, Wu Y, Dong S, Wu Z. Plant immunity suppressor SKRP encodes a novel RNA-binding protein that targets exon 3' end of unspliced RNA. THE NEW PHYTOLOGIST 2023; 240:1467-1483. [PMID: 37658678 DOI: 10.1111/nph.19236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The regulatory roles of RNA splicing in plant immunity are emerging but still largely obscure. We reported previously that Phytophthora pathogen effector Avr3c targets a soybean protein SKRP (serine/lysine/arginine-rich protein) to impair soybean basal immunity by regulating host pre-mRNA alternative splicing, while the biochemical nature of SKRP remains unknown. Here, by using Arabidopsis as a model, we studied the mechanism of SKRP in regulating pre-mRNA splicing and plant immunity. AtSKRP confers impaired plant immunity against Phytophthora capsici and associates with spliceosome component PRP8 and splicing factor SR45, which positively and negatively regulate plant immunity, respectively. Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) showed AtSKRP is a novel RNA-binding protein that targets exon 3' end of unspliced RNA. Such position-specific binding of SKRP is associated with its activity in suppressing intron retention, including at positive immune regulatory genes UBP25 and RAR1. In addition, we found AtSKRP self-interact and forms oligomer, and these properties are associated with its function in plant immunity. Overall, our findings reveal that the immune repressor SKRP is a spliceosome-associated protein that targets exon 3' end to regulate pre-mRNA splicing in Arabidopsis.
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Affiliation(s)
- Ling Chen
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhihui Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Huang
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufan Hui
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yufeng Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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6
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Rouvière JO, Salerno-Kochan A, Lykke-Andersen S, Garland W, Dou Y, Rathore O, Molska EŠ, Wu G, Schmid M, Bugai A, Jakobsen L, Žumer K, Cramer P, Andersen JS, Conti E, Jensen TH. ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts. Mol Cell 2023:S1097-2765(23)00384-2. [PMID: 37329882 DOI: 10.1016/j.molcel.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif (SLiM) in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit RNAPII termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. We find that ZC3H4, in turn, forms a direct connection to the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay.
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Affiliation(s)
- Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Søren Lykke-Andersen
- 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
| | - Yuhui Dou
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Ewa Šmidová Molska
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Andrii Bugai
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kristina Žumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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7
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Temporal-iCLIP captures co-transcriptional RNA-protein interactions. Nat Commun 2023; 14:696. [PMID: 36755023 PMCID: PMC9908952 DOI: 10.1038/s41467-023-36345-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5'end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3'end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.
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8
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Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
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Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
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9
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Kieffer F, Hilal F, Gay AS, Debayle D, Pronot M, Poupon G, Lacagne I, Bardoni B, Martin S, Gwizdek C. Combining affinity purification and mass spectrometry to define the network of the nuclear proteins interacting with the N-terminal region of FMRP. Front Mol Biosci 2022; 9:954087. [PMID: 36237573 PMCID: PMC9553004 DOI: 10.3389/fmolb.2022.954087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-Syndrome (FXS) represents the most common inherited form of intellectual disability and the leading monogenic cause of Autism Spectrum Disorders. In most cases, this disease results from the absence of expression of the protein FMRP encoded by the FMR1 gene (Fragile X messenger ribonucleoprotein 1). FMRP is mainly defined as a cytoplasmic RNA-binding protein regulating the local translation of thousands of target mRNAs. Interestingly, FMRP is also able to shuttle between the nucleus and the cytoplasm. However, to date, its roles in the nucleus of mammalian neurons are just emerging. To broaden our insight into the contribution of nuclear FMRP in mammalian neuronal physiology, we identified here a nuclear interactome of the protein by combining subcellular fractionation of rat forebrains with pull‐ down affinity purification and mass spectrometry analysis. By this approach, we listed 55 candidate nuclear partners. This interactome includes known nuclear FMRP-binding proteins as Adar or Rbm14 as well as several novel candidates, notably Ddx41, Poldip3, or Hnrnpa3 that we further validated by target‐specific approaches. Through our approach, we identified factors involved in different steps of mRNA biogenesis, as transcription, splicing, editing or nuclear export, revealing a potential central regulatory function of FMRP in the biogenesis of its target mRNAs. Therefore, our work considerably enlarges the nuclear proteins interaction network of FMRP in mammalian neurons and lays the basis for exciting future mechanistic studies deepening the roles of nuclear FMRP in neuronal physiology and the etiology of the FXS.
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Affiliation(s)
- Félicie Kieffer
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fahd Hilal
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Anne-Sophie Gay
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Marie Pronot
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Gwénola Poupon
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Iliona Lacagne
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Stéphane Martin
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Carole Gwizdek
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- *Correspondence: Carole Gwizdek,
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10
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Gerlach P, Garland W, Lingaraju M, Salerno-Kochan A, Bonneau F, Basquin J, Jensen TH, Conti E. Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome. Mol Cell 2022; 82:2505-2518.e7. [PMID: 35688157 PMCID: PMC9278407 DOI: 10.1016/j.molcel.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/07/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3′ end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome. NEXT homodimerizes through two intertwined ZCCHC8 subunits ZCCHC8 binds MTR4 with both constitutive and regulatory interactions Stable MTR4 arch interactions orient the two helicases in opposite directions Regulatory interactions at the MTR4 helicase domain guide RNA to the exosome
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Affiliation(s)
- Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
| | - William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
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11
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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12
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Lange H, Gagliardi D. Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. THE PLANT CELL 2022; 34:967-988. [PMID: 34954803 PMCID: PMC8894942 DOI: 10.1093/plcell/koab310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 05/08/2023]
Abstract
RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.
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Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Author for correspondence:
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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13
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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14
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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15
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Ghosh G, Samui S, Das S, Singh V, Pal D, Das S, Naskar J, Sinha Roy S, Basu U. Poly C Binding Protein 2 dependent nuclear retention of the utrophin-A mRNA in C2C12 cells. RNA Biol 2021; 18:612-622. [PMID: 34904931 PMCID: PMC8782177 DOI: 10.1080/15476286.2021.2004683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD.
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Affiliation(s)
- Gargi Ghosh
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Satyabrata Samui
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Vandana Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, New Delhi, India
| | - Doel Pal
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Subhanwita Das
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India
| | - Jishu Naskar
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, New Delhi, India
| | - Utpal Basu
- Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, India,CONTACT Utpal Basu Department of Molecular Biology & Biotechnology, University of Kalyani, Kalyani, West Bengal741235, India
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16
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Ofir-Birin Y, Ben Ami Pilo H, Cruz Camacho A, Rudik A, Rivkin A, Revach OY, Nir N, Block Tamin T, Abou Karam P, Kiper E, Peleg Y, Nevo R, Solomon A, Havkin-Solomon T, Rojas A, Rotkopf R, Porat Z, Avni D, Schwartz E, Zillinger T, Hartmann G, Di Pizio A, Quashie NB, Dikstein R, Gerlic M, Torrecilhas AC, Levy C, Nolte-'t Hoen ENM, Bowie AG, Regev-Rudzki N. Malaria parasites both repress host CXCL10 and use it as a cue for growth acceleration. Nat Commun 2021; 12:4851. [PMID: 34381047 PMCID: PMC8357946 DOI: 10.1038/s41467-021-24997-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
Pathogens are thought to use host molecular cues to control when to initiate life-cycle transitions, but these signals are mostly unknown, particularly for the parasitic disease malaria caused by Plasmodium falciparum. The chemokine CXCL10 is present at high levels in fatal cases of cerebral malaria patients, but is reduced in patients who survive and do not have complications. Here we show a Pf 'decision-sensing-system' controlled by CXCL10 concentration. High CXCL10 expression prompts P. falciparum to initiate a survival strategy via growth acceleration. Remarkably, P. falciparum inhibits CXCL10 synthesis in monocytes by disrupting the association of host ribosomes with CXCL10 transcripts. The underlying inhibition cascade involves RNA cargo delivery into monocytes that triggers RIG-I, which leads to HUR1 binding to an AU-rich domain of the CXCL10 3'UTR. These data indicate that when the parasite can no longer keep CXCL10 at low levels, it can exploit the chemokine as a cue to shift tactics and escape.
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Affiliation(s)
- Yifat Ofir-Birin
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Ben Ami Pilo
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Abel Cruz Camacho
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ariel Rudik
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Rivkin
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Or-Yam Revach
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Nir
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Block Tamin
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Paula Abou Karam
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Edo Kiper
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Structural Proteomics Unit, Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Reinat Nevo
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Aryeh Solomon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Havkin-Solomon
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alicia Rojas
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dror Avni
- The Institute of Geographic Medicine and Tropical Diseases and the Laboratory for Tropical Diseases Research, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eli Schwartz
- The Institute of Geographic Medicine and Tropical Diseases and the Laboratory for Tropical Diseases Research, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Technical University of Munich, Freising, Germany
| | - Neils Ben Quashie
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
- Centre for Tropical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana
| | - Rivka Dikstein
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ana Claudia Torrecilhas
- Department of Pharmaceutical Sciences, Federal University of São Paulo, UNIFESP, Diadema, Brazil
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | - Esther N M Nolte-'t Hoen
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Neta Regev-Rudzki
- Faculty of Biochemistry, Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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17
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ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Biochem Soc Trans 2021; 49:1325-1336. [PMID: 34060620 DOI: 10.1042/bst20201008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/26/2023]
Abstract
ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.
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18
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Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Res 2021; 31:1106-1119. [PMID: 33832989 PMCID: PMC8168582 DOI: 10.1101/gr.273904.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/01/2021] [Indexed: 12/24/2022]
Abstract
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 (Gabbr1) are highly expressed in mESCs but are absent from the cytoplasm. Instead, incompletely spliced Gabbr1 RNA remains sequestered on chromatin, where it is bound by PTBP1, similar to certain long noncoding RNAs. Upon neuronal differentiation, Gabbr1 RNA becomes fully processed and exported for translation. Thus, splicing repression and chromatin anchoring of RNA combine to allow posttranscriptional regulation of Gabbr1 over development. For this and other genes, polyadenylated RNA abundance does not indicate functional gene expression. Our data sets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
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Affiliation(s)
- Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, California 90095, USA.,Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Han Young Lim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
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19
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Abstract
The subcellular localization of RNAs correlates with their function and how they are regulated. Most protein-coding mRNAs are exported into the cytoplasm for protein synthesis, while some mRNA species, long noncoding RNAs, and some regulatory element-associated unstable transcripts tend to be retained in the nucleus, where they function as a regulatory unit and/or are regulated by nuclear surveillance pathways. While the mechanisms regulating mRNA export and localization have been well summarized, the mechanisms governing nuclear retention of RNAs, especially of noncoding RNAs, are seldomly reviewed. In this review, we summarize recent advances in the mechanistic study of RNA nuclear retention, especially for noncoding RNAs, from the angle of cis-acting elements embedded in RNA transcripts and their interaction with trans-acting factors. We also try to illustrate the general principles of RNA nuclear retention and we discuss potential areas for future investigation.
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Affiliation(s)
- Chong Tong
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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20
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Zhang L, Li C, Su X. Emerging impact of the long noncoding RNA MIR22HG on proliferation and apoptosis in multiple human cancers. J Exp Clin Cancer Res 2020; 39:271. [PMID: 33267888 PMCID: PMC7712612 DOI: 10.1186/s13046-020-01784-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
An increasing number of studies have shown that long noncoding RNAs (lncRNAs) play important roles in diverse cellular processes, including proliferation, apoptosis, migration, invasion, chromatin remodeling, metabolism and immune escape. Clinically, the expression of MIR22HG is increased in many human tumors (colorectal cancer, gastric cancer, hepatocellular carcinoma, lung cancer, and thyroid carcinoma), while in others (esophageal adenocarcinoma and glioblastoma), it is significantly decreased. Moreover, MIR22HG has been reported to function as a competitive endogenous RNA (ceRNA), be involved in signaling pathways, interact with proteins and interplay with miRNAs as a host gene to participate in tumorigenesis and tumor progression. In this review, we describe the biological functions of MIR22HG, reveal its underlying mechanisms for cancer regulation, and highlight the potential role of MIR22HG as a novel cancer prognostic biomarker and therapeutic target that can increase the efficacy of immunotherapy and targeted therapy for cancer treatment.
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Affiliation(s)
- Le Zhang
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, 1 Tong Dao Street, Huimin District, Inner Mongolia, 010050, Hohhot, China
| | - Cuixia Li
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, 1 Tong Dao Street, Huimin District, Inner Mongolia, 010050, Hohhot, China
| | - Xiulan Su
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, 1 Tong Dao Street, Huimin District, Inner Mongolia, 010050, Hohhot, China.
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21
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Desideri F, Cipriano A, Petrezselyova S, Buonaiuto G, Santini T, Kasparek P, Prochazka J, Janson G, Paiardini A, Calicchio A, Colantoni A, Sedlacek R, Bozzoni I, Ballarino M. Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1. Cell Rep 2020; 33:108548. [PMID: 33357424 PMCID: PMC7773549 DOI: 10.1016/j.celrep.2020.108548] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Chromatin architect of muscle expression (Charme) is a muscle-restricted long noncoding RNA (lncRNA) that plays an important role in myogenesis. Earlier evidence indicates that the nuclear Charme isoform, named pCharme, acts on the chromatin by assisting the formation of chromatin domains where myogenic transcription occurs. By combining RNA antisense purification (RAP) with mass spectrometry and loss-of-function analyses, we have now identified the proteins that assist these chromatin activities. These proteins—which include a sub-set of splicing regulators, principally PTBP1 and the multifunctional RNA/DNA binding protein MATR3—bind to sequences located within the alternatively spliced intron-1 to form nuclear aggregates. Consistent with the functional importance of pCharme interactome in vivo, a targeted deletion of the intron-1 by a CRISPR-Cas9 approach in mouse causes the release of pCharme from the chromatin and results in cardiac defects similar to what was observed upon knockout of the full-length transcript. pCharme is the chromatin-retained isoform of the muscle-specific Charme lncRNA Intronic signals coordinate the association of pCharme with MATR3 and PTBP1 The particle assembly prompts pCharme intron-1 chromatin retention Deletion of the intron-1 by CRISPR-Cas9 leads to heart defects in mouse
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Affiliation(s)
- Fabio Desideri
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Andrea Cipriano
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Silvia Petrezselyova
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giulia Buonaiuto
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Petr Kasparek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giacomo Janson
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Calicchio
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Irene Bozzoni
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.
| | - Monica Ballarino
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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Palazzo AF, Kang YM. GC-content biases in protein-coding genes act as an "mRNA identity" feature for nuclear export. Bioessays 2020; 43:e2000197. [PMID: 33165929 DOI: 10.1002/bies.202000197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/11/2023]
Abstract
It has long been observed that human protein-coding genes have a particular distribution of GC-content: the 5' end of these genes has high GC-content while the 3' end has low GC-content. In 2012, it was proposed that this pattern of GC-content could act as an mRNA identity feature that would lead to it being better recognized by the cellular machinery to promote its nuclear export. In contrast, junk RNA, which largely lacks this feature, would be retained in the nucleus and targeted for decay. Now two recent papers have provided evidence that GC-content does promote the nuclear export of many mRNAs in human cells.
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Affiliation(s)
- Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
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23
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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24
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Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V, Jensen TH, Sandelin A. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res 2020; 48:8509-8528. [PMID: 32710631 PMCID: PMC7470964 DOI: 10.1093/nar/gkaa594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Evdoxia Karadoulama
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.,European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jerome Olivier Rouviere
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Christian Skov Vaagensø
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Martin Moravec
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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25
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Kaposi's Sarcoma-Associated Herpesvirus Fine-Tunes the Temporal Expression of Late Genes by Manipulating a Host RNA Quality Control Pathway. J Virol 2020; 94:JVI.00287-20. [PMID: 32376621 DOI: 10.1128/jvi.00287-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/28/2020] [Indexed: 12/25/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic nuclear DNA virus that expresses its genes using the host cell transcription and RNA processing machinery. As a result, KSHV transcripts are subject to degradation by at least two host-mediated nuclear RNA decay pathways, the PABPN1- and poly(A) polymerase α/γ (PAPα/γ)-mediated RNA decay (PPD) pathway and an ARS2-dependent decay pathway. Here, we present global analyses of viral transcript levels to further understand the roles of these decay pathways in KSHV gene expression. Consistent with our recent report that the KSHV ORF57 protein increases viral transcript stability by impeding ARS2-dependent decay, ARS2 knockdown has only modest effects on viral gene expression 24 h after lytic reactivation of wild-type virus. In contrast, inactivation of PPD has more widespread effects, including premature accumulation of late transcripts. The upregulation of late transcripts does not require the primary late-gene-specific viral transactivation factor, suggesting that cryptic transcription produces the transcripts that then succumb to PPD. Remarkably, PPD inactivation has no effect on late transcripts at their proper time of expression. We show that this time-dependent PPD evasion by late transcripts requires the host factor nuclear RNAi-defective 2 (NRDE2), which has previously been reported to protect cellular RNAs by sequestering decay factors. From these studies, we conclude that KSHV uses PPD to fine-tune the temporal expression of its genes by preventing their premature accumulation.IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus that causes Kaposi's sarcoma and other lymphoproliferative disorders. Nuclear expression of KSHV genes results in exposure to at least two host-mediated nuclear RNA decay pathways, the PABPN1- and PAPα/γ-mediated RNA decay (PPD) pathway and an ARS2-mediated decay pathway. Perhaps unsurprisingly, we previously found that KSHV uses specific mechanisms to protect its transcripts from ARS2-mediated decay. In contrast, here we show that PPD is required to dampen the expression of viral late transcripts that are prematurely transcribed, presumably due to cryptic transcription early in infection. At the proper time for their expression, KSHV late transcripts evade PPD through the activity of the host factor NRDE2. We conclude that KSHV fine-tunes the temporal expression of its genes by modulating PPD activity. Thus, the virus both protects from and exploits the host nuclear RNA decay machinery for proper expression of its genes.
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