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The POLR3G Subunit of Human RNA Polymerase III Regulates Tumorigenesis and Metastasis in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14235732. [PMID: 36497214 PMCID: PMC9735567 DOI: 10.3390/cancers14235732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes short untranslated RNAs that contribute to the regulation of gene expression. Two isoforms of human Pol III have been described that differ by the presence of the POLR3G/RPC32α or POLR3GL/RPC32β subunits. POLR3G was found to be expressed in embryonic stem cells and at least a subset of transformed cells, whereas POLR3GL shows a ubiquitous expression pattern. Here, we demonstrate that POLR3G is specifically overexpressed in clinical samples of triple-negative breast cancer (TNBC) but not in other molecular subtypes of breast cancer. POLR3G KO in the MDA-MB231 TNBC cell line dramatically reduces anchorage-independent growth and invasive capabilities in vitro. In addition, the POLR3G KO impairs tumor growth and metastasis formation of orthotopic xenografts in mice. Moreover, KO of POLR3G induces expression of the pioneer transcription factor FOXA1 and androgen receptor. In contrast, the POLR3G KO neither alters proliferation nor the expression of epithelial-mesenchymal transition marker genes. These data demonstrate that POLR3G expression is required for TNBC tumor growth, invasiveness and dissemination and that its deletion affects triple-negative breast cancer-specific gene expression.
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2
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Sun J, Li X, Hou X, Cao S, Cao W, Zhang Y, Song J, Wang M, Wang H, Yan X, Li Z, Roeder RG, Wang W. Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Nat Commun 2022; 13:6871. [PMID: 36369505 PMCID: PMC9652321 DOI: 10.1038/s41467-022-34639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system.
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Affiliation(s)
- Jianfeng Sun
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Xue Li
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xuben Hou
- grid.27255.370000 0004 1761 1174School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Sujian Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Wenjin Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Ye Zhang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Jinyang Song
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Manfu Wang
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Hao Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xiaodong Yan
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Zengpeng Li
- grid.453137.70000 0004 0406 0561Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Robert G. Roeder
- grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Wei Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Interventional Medicine Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033 China
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3
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Zhang J, Cavallaro M, Hebenstreit D. Timing RNA polymerase pausing with TV-PRO-seq. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723238 PMCID: PMC8547241 DOI: 10.1016/j.crmeth.2021.100083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally engaged polymerases. This is known to mainly occur in promoter-proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. We present here the time-variant precision nuclear run-on and sequencing (TV-PRO-seq) assay, an extension of the standard PRO-seq that allows us to estimate genome-wide pausing times at single-base resolution. Its application to human cells demonstrates that, proximal to promoters, polymerases pause more frequently but for shorter times than in other genomic regions. Comparison with single-cell gene expression data reveals that the polymerase pausing times are longer in highly expressed genes, while transcriptionally noisier genes have higher pausing frequencies and slightly longer pausing times. Analyses of histone modifications suggest that the marker H3K36me3 is related to the polymerase pausing.
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Affiliation(s)
- Jie Zhang
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
| | - Massimo Cavallaro
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
- Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, the University of Warwick, CV4 7AL Coventry, UK
| | - Daniel Hebenstreit
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
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4
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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Lytic Infection with Murine Gammaherpesvirus 68 Activates Host and Viral RNA Polymerase III Promoters and Enhances Noncoding RNA Expression. J Virol 2021; 95:e0007921. [PMID: 33910955 PMCID: PMC8223928 DOI: 10.1128/jvi.00079-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase III (pol III) transcribes multiple noncoding RNAs (ncRNAs) that are essential for cellular function. Pol III-dependent transcription is also engaged during certain viral infections, including those of the gammaherpesviruses (γHVs), where pol III-dependent viral ncRNAs promote pathogenesis. Additionally, several host ncRNAs are upregulated during γHV infection and play integral roles in pathogenesis by facilitating viral establishment and gene expression. Here, we sought to investigate how pol III promoters and transcripts are regulated during gammaherpesvirus infection using the murine gammaherpesvirus 68 (γHV68) system. To compare the transcription of host and viral pol III-dependent ncRNAs, we analyzed a series of pol III promoters for host and viral ncRNAs using a luciferase reporter optimized to measure pol III activity. We measured promoter activity from the reporter gene at the translation level via luciferase activity and at the transcription level via reverse transcription-quantitative PCR (RT-qPCR). We further measured endogenous ncRNA expression at single-cell resolution by flow cytometry. These studies demonstrated that lytic infection with γHV68 increased the transcription from multiple host and viral pol III promoters and further identified the ability of accessory sequences to influence both baseline and inducible promoter activity after infection. RNA flow cytometry revealed the induction of endogenous pol III-derived ncRNAs that tightly correlated with viral gene expression. These studies highlight how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to increase pol III-derived RNAs, a process that may further modify cellular function and enhance viral gene expression and pathogenesis. IMPORTANCE Gammaherpesviruses are a prime example of how viruses can alter the host transcriptional landscape to establish infection. Despite major insights into how these viruses modify RNA polymerase II-dependent generation of messenger RNAs, how these viruses influence the activity of host RNA polymerase III remains much less clear. Small noncoding RNAs produced by RNA polymerase III are increasingly recognized to play critical regulatory roles in cell biology and virus infection. Studies of RNA polymerase III-dependent transcription are complicated by multiple promoter types and diverse RNAs with variable stability and processing requirements. Here, we characterized a reporter system to directly study RNA polymerase III-dependent responses during gammaherpesvirus infection and utilized single-cell flow cytometry-based methods to reveal that gammaherpesvirus lytic replication broadly induces pol III activity to enhance host and viral noncoding RNA expression within the infected cell.
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6
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Wang Q, Li S, Wan F, Xu Y, Wu Z, Cao M, Lan P, Lei M, Wu J. Structural insights into transcriptional regulation of human RNA polymerase III. Nat Struct Mol Biol 2021; 28:220-227. [PMID: 33558766 DOI: 10.1038/s41594-021-00557-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/29/2020] [Indexed: 01/30/2023]
Abstract
RNA polymerase III (Pol III) synthesizes structured, essential small RNAs, such as transfer RNA, 5S ribosomal RNA and U6 small nuclear RNA. Pol III, the largest nuclear RNA polymerase, is composed of a conserved core region and eight constitutive regulatory subunits, but how these factors jointly regulate Pol III transcription remains unclear. Here, we present cryo-EM structures of human Pol III in both apo and elongating states, which unveil both an orchestrated movement during the apo-to-elongating transition and an unexpected apo state in which the RPC7 subunit tail occupies the DNA-RNA-binding cleft of Pol III, suggesting that RPC7 plays important roles in both autoinhibition and transcription initiation. The structures also reveal a proofreading mechanism for the TFIIS-like subunit RPC10, which stably retains its catalytic position in the secondary channel, explaining the high fidelity of Pol III transcription. Our work provides an integrated picture of the mechanism of Pol III transcription regulation.
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Affiliation(s)
- Qianmin Wang
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Shaobai Li
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Futang Wan
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Youwei Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Zhenfang Wu
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Mi Cao
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Pengfei Lan
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Institute of Precision Medicine, Shanghai, China.
| | - Ming Lei
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Institute of Precision Medicine, Shanghai, China. .,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian Wu
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Institute of Precision Medicine, Shanghai, China.
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7
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Gene-Specific Control of tRNA Expression by RNA Polymerase II. Mol Cell 2020; 78:765-778.e7. [PMID: 32298650 DOI: 10.1016/j.molcel.2020.03.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/12/2020] [Accepted: 03/13/2020] [Indexed: 12/20/2022]
Abstract
Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.
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8
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Ayoubi LE, Dumay-Odelot H, Chernev A, Boissier F, Minvielle-Sébastia L, Urlaub H, Fribourg S, Teichmann M. The hRPC62 subunit of human RNA polymerase III displays helicase activity. Nucleic Acids Res 2019; 47:10313-10326. [PMID: 31529052 PMCID: PMC6821166 DOI: 10.1093/nar/gkz788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 11/20/2022] Open
Abstract
In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3′-5′ DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα.
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Affiliation(s)
- Leyla El Ayoubi
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- Correspondence may also be addressed to Hélène Dumay-Odelot.
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Fanny Boissier
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | | | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Strasse 420, 37075 Göttingen, Germany
| | - Sébastien Fribourg
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Martin Teichmann
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- To whom correspondence should be addressed. Tel: +33 5 5757 4647;
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9
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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10
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Choquet K, Forget D, Meloche E, Dicaire MJ, Bernard G, Vanderver A, Schiffmann R, Fabian MR, Teichmann M, Coulombe B, Brais B, Kleinman CL. Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200. J Biol Chem 2019; 294:7445-7459. [PMID: 30898877 PMCID: PMC6509492 DOI: 10.1074/jbc.ra118.006271] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small noncoding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3–HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has so far been elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A→G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3–HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.
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Affiliation(s)
- Karine Choquet
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Diane Forget
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Elisabeth Meloche
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Marie-Josée Dicaire
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Geneviève Bernard
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,Pediatrics, McGill University, Montréal, Québec H3A 0G4, Canada.,the Department of Internal Medicine, Division of Medical Genetics, Montréal Children's Hospital, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Child Health and Human Development Program, and.,MyeliNeuroGene Laboratory, Research Institute, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Departments of Neurology and Neurosurgery and
| | - Adeline Vanderver
- the Division of Neurology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania 19104
| | - Raphael Schiffmann
- the Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas 75204
| | - Marc R Fabian
- the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Martin Teichmann
- INSERM U1212-CNRS UMR5320, Université de Bordeaux, Bordeaux, France, and
| | - Benoit Coulombe
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada.,the Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Bernard Brais
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada.,the Departments of Neurology and Neurosurgery and
| | - Claudia L Kleinman
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada, .,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
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11
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Dorboz I, Dumay-Odelot H, Boussaid K, Bouyacoub Y, Barreau P, Samaan S, Jmel H, Eymard-Pierre E, Cances C, Bar C, Poulat AL, Rousselle C, Renaldo F, Elmaleh-Bergès M, Teichmann M, Boespflug-Tanguy O. Mutation in POLR3K causes hypomyelinating leukodystrophy and abnormal ribosomal RNA regulation. NEUROLOGY-GENETICS 2018; 4:e289. [PMID: 30584594 PMCID: PMC6283457 DOI: 10.1212/nxg.0000000000000289] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/05/2018] [Indexed: 11/17/2022]
Abstract
Objective To identify the genetic cause of hypomyelinating leukodystrophy in 2 consanguineous families. Methods Homozygosity mapping combined with whole-exome sequencing of consanguineous families was performed. Mutation consequences were determined by studying the structural change of the protein and by the RNA analysis of patients' fibroblasts. Results We identified a biallelic mutation in a gene coding for a Pol III–specific subunit, POLR3K (c.121C>T/p.Arg41Trp), that cosegregates with the disease in 2 unrelated patients. Patients expressed neurologic and extraneurologic signs found in POLR3A- and POLR3B-related leukodystrophies with a peculiar severe digestive dysfunction. The mutation impaired the POLR3K-POLR3B interactions resulting in zebrafish in abnormal gut development. Functional studies in the 2 patients' fibroblasts revealed a severe decrease (60%–80%) in the expression of 5S and 7S ribosomal RNAs in comparison with control. Conclusions These analyses underlined the key role of ribosomal RNA regulation in the development and maintenance of the white matter and the cerebellum as already reported for diseases related to genes involved in transfer RNA or translation initiation factors.
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Affiliation(s)
- Imen Dorboz
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Hélene Dumay-Odelot
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Karima Boussaid
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Yosra Bouyacoub
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Pauline Barreau
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Simon Samaan
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Haifa Jmel
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Eleonore Eymard-Pierre
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Claude Cances
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Céline Bar
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Anne-Lise Poulat
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Christophe Rousselle
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Florence Renaldo
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Monique Elmaleh-Bergès
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Martin Teichmann
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Odile Boespflug-Tanguy
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
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Durrieu-Gaillard S, Dumay-Odelot H, Boldina G, Tourasse NJ, Allard D, André F, Macari F, Choquet A, Lagarde P, Drutel G, Leste-Lasserre T, Petitet M, Lesluyes T, Lartigue-Faustin L, Dupuy JW, Chibon F, Roeder RG, Joubert D, Vagner S, Teichmann M. Regulation of RNA polymerase III transcription during transformation of human IMR90 fibroblasts with defined genetic elements. Cell Cycle 2018; 17:605-615. [PMID: 29171785 DOI: 10.1080/15384101.2017.1405881] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs that are essential for cellular homeostasis and growth. Its activity is regulated by inactivation of tumor suppressor proteins and overexpression of the oncogene c-MYC, but the concerted action of these tumor-promoting factors on Pol III transcription has not yet been assessed. In order to comprehensively analyse the regulation of Pol III transcription during tumorigenesis we employ a model system that relies on the expression of five genetic elements to achieve cellular transformation. Expression of these elements in six distinct transformation intermediate cell lines leads to the inactivation of TP53, RB1, and protein phosphatase 2A, as well as the activation of RAS and the protection of telomeres by TERT, thereby conducting to full tumoral transformation of IMR90 fibroblasts. Transformation is accompanied by moderately enhanced levels of a subset of Pol III-transcribed RNAs (7SK; MRP; H1). In addition, mRNA and/or protein levels of several Pol III subunits and transcription factors are upregulated, including increased protein levels of TFIIIB and TFIIIC subunits, of SNAPC1 and of Pol III subunits. Strikingly, the expression of POLR3G and of SNAPC1 is strongly enhanced during transformation in this cellular transformation model. Collectively, our data indicate that increased expression of several components of the Pol III transcription system accompanied by a 2-fold increase in steady state levels of a subset of Pol III RNAs is sufficient for sustaining tumor formation.
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Affiliation(s)
- Stéphanie Durrieu-Gaillard
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Hélène Dumay-Odelot
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Galina Boldina
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France.,c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Nicolas J Tourasse
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Delphine Allard
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Fabrice André
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Françoise Macari
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Armelle Choquet
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Pauline Lagarde
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France.,g Université de Bordeaux , F-33076 Bordeaux , France
| | - Guillaume Drutel
- h NeuroCentre François Magendie , INSERM U862 , F-33077 Bordeaux , France
| | | | - Marion Petitet
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France
| | - Tom Lesluyes
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Lydia Lartigue-Faustin
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Jean-William Dupuy
- i Université de Bordeaux , Plateforme Protéome - Centre Génomique Fonctionnelle Bordeaux , 33076 Bordeaux , France
| | - Frédéric Chibon
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Robert G Roeder
- j The Rockefeller University , 1230 York Avenue, New York , NY 10065 , USA
| | - Dominique Joubert
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Stéphan Vagner
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France.,k Institut Curie , CNRS UMR 3348, F-91405 Orsay , France
| | - Martin Teichmann
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
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13
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Willis IM, Moir RD. Signaling to and from the RNA Polymerase III Transcription and Processing Machinery. Annu Rev Biochem 2018; 87:75-100. [PMID: 29328783 DOI: 10.1146/annurev-biochem-062917-012624] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities. In this review, we consider how nutrients and stress control Pol III transcription via its factors and its negative regulator, Maf1. We highlight recent work showing that the composition of the tRNA population and the function of individual tRNAs is dynamically controlled and that unrestrained Pol III transcription can reprogram central metabolic pathways.
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Affiliation(s)
- Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , .,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; ,
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14
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Boissier F, Dumay-Odelot H, Teichmann M, Fribourg S. Structural analysis of human RPC32β-RPC62 complex. J Struct Biol 2015; 192:313-319. [PMID: 26394183 DOI: 10.1016/j.jsb.2015.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 01/22/2023]
Abstract
Transcription initiation by eukaryotic RNA polymerase (Pol) III relies on the subcomplex RPC62/RPC39/RPC32. Two distinct isoforms of RPC32 are encoded in the human genome. RPC32α expression is highly regulated and found only in stem cells and transformed cells, whereas RPC32β is ubiquitously expressed in tissues. Here we identify a core-interacting domain of RPC32 sufficient for the interaction with RPC62. We present the crystal structure of a complex of RPC62 and the RPC32β core domain. RPC32β associates with the extended winged helix 1 and 2 and the coiled coil domain of RPC62 qualifying RPC32 as a molecular bridge in between RPC62 domains. The RPC62-RPC32 complex fit into EM data suggests a bi-functional role for RPC32 through interactions with the largest Pol III subunit and through solvent exposed residues. RPC32 positioning into Pol III suggests that subunit-specific contacts at the surface of the Pol III holoenzyme are critical for its function.
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Affiliation(s)
- Fanny Boissier
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM - U869, ARNA Laboratory, F-33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; INSERM, U869, ARNA Laboratory, Equipe Labellisée Contre le Cancer, F-33076 Bordeaux, France
| | - Martin Teichmann
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; INSERM, U869, ARNA Laboratory, Equipe Labellisée Contre le Cancer, F-33076 Bordeaux, France
| | - Sébastien Fribourg
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM - U869, ARNA Laboratory, F-33000 Bordeaux, France.
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Duttke SHC. RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro. J Biol Chem 2014; 289:20396-404. [PMID: 24917680 DOI: 10.1074/jbc.m114.563254] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In eukaryotes, there are three major RNA polymerases (Pol) in the nucleus, which are commonly described as transcribing non-overlapping subsets of genes. Structural studies have highlighted a conserved core shared among all three transcription systems. Initiation of human Pol III from TATA box-containing Pol II promoters under conditions with impaired Pol II transcription activity have been described previously. RNA polymerase III and Pol II were found to co-localize at the promoters of the c-myc gene and the RPPH1 sRNA in vivo. Here, I report that Pol III can, like Pol II, initiate transcription from most tested Pol II core promoters when assayed with crude human nuclear extracts (HSK, SNF, or Dignam). Both polymerases often initiate from the same transcription start site, and depend on a TATA box or AT-rich region but not the downstream promoter element (DPE) or the motif ten element (MTE). Moderate (∼2-fold) changes in the ratio of DNA template to nuclear extract were sufficient to change Pol II-mediated transcription to a mixture of Pol II- and Pol III-, or to a solely Pol III-dependent initiation of transcription from Pol II promoters. Polymerase specificity is thus not fixed but a variable that depends on the properties of the promoter and the transcription conditions. These findings provide functional evidence for a close similarity between the Pol II and Pol III transcription complexes, and additionally explain previous controversies in the literature.
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Affiliation(s)
- Sascha H C Duttke
- From the Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
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