1
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Kao TL, Huang YC, Chen YH, Baumann P, Tseng CK. LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis. Nat Commun 2024; 15:5955. [PMID: 39009594 PMCID: PMC11250828 DOI: 10.1038/s41467-024-50422-w] [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: 09/21/2023] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
Human telomerase assembly is a highly dynamic process. Using biochemical approaches, we find that LARP3 and LARP7/MePCE are involved in the early stage of human telomerase RNA (hTR) and that their binding to RNA is destabilized when the mature form is produced. LARP3 plays a negative role in preventing the processing of the 3'-extended long (exL) form and the binding of LARP7 and MePCE. Interestingly, the tertiary structure of the exL form prevents LARP3 binding and facilitates hTR biogenesis. Furthermore, low levels of LARP3 promote hTR maturation, increase telomerase activity, and elongate telomeres. LARP7 and MePCE depletion inhibits the conversion of the 3'-extended short (exS) form into mature hTR and the cytoplasmic accumulation of hTR, resulting in telomere shortening. Taken together our data suggest that LARP3 and LARP7/MePCE mediate the processing of hTR precursors and regulate the production of functional telomerase.
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Affiliation(s)
- Tsai-Ling Kao
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Cheng Huang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsuan Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Peter Baumann
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Chi-Kang Tseng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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2
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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3
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Amir N, Taube R. Role of long noncoding RNA in regulating HIV infection-a comprehensive review. mBio 2024; 15:e0192523. [PMID: 38179937 PMCID: PMC10865847 DOI: 10.1128/mbio.01925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A complete cure against human immunodeficiency virus (HIV) infection remains out of reach, as the virus persists in stable cell reservoirs that are resistant to antiretroviral therapy. The key to eliminating these reservoirs lies in deciphering the processes that govern viral gene expression and latency. However, while we comprehensively understand how host proteins influence HIV gene expression and viral latency, the emerging role of long noncoding RNAs (lncRNAs) in the context of T cell activation, HIV gene expression, and viral latency remain unexplored. This review dives into the evolving significance of lncRNAs and their impact on HIV gene expression and viral latency. We provide an overview of the current knowledge regarding how lncRNAs regulate HIV gene expression, categorizing them as either activators or inhibitors of viral gene expression and infectivity. Furthermore, we offer insights into the potential therapeutic applications of lncRNAs in combatting HIV. A deeper understanding of how lncRNAs modulate HIV gene transcription holds promise for developing novel RNA-based therapies to complement existing treatment strategies to eradicate HIV reservoirs.
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Affiliation(s)
- Noa Amir
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
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4
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Palumbo RJ, Yang Y, Feigon J, Hanes SD. Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. Genetics 2024; 226:iyad203. [PMID: 37982586 PMCID: PMC10763541 DOI: 10.1093/genetics/iyad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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5
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Sanz-Álvarez M, Luque M, Morales-Gallego M, Cristóbal I, Ramírez-Merino N, Rangel Y, Izarzugaza Y, Eroles P, Albanell J, Madoz-Gúrpide J, Rojo F. Generation and Characterization of Trastuzumab/Pertuzumab-Resistant HER2-Positive Breast Cancer Cell Lines. Int J Mol Sci 2023; 25:207. [PMID: 38203378 PMCID: PMC10779249 DOI: 10.3390/ijms25010207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The combination of trastuzumab and pertuzumab as first-line therapy in patients with HER2-positive breast cancer has shown significant clinical benefits compared to trastuzumab alone. However, despite initial therapeutic success, most patients eventually progress, and tumors develop acquired resistance and invariably relapse. Therefore, there is an urgent need to improve our understanding of the mechanisms governing resistance in order to develop targeted therapeutic strategies with improved efficacy. We generated four novel HER2-positive cell lines via prolonged exposure to trastuzumab and pertuzumab and determined their resistance rates. Long-term resistance was confirmed by a significant increase in the colony-forming capacity of the derived cells. We authenticated the molecular identity of the new lines via both immunohistochemistry for the clinical phenotype and molecular profiling of point mutations. HER2 overexpression was confirmed in all resistant cell lines, and acquisition of resistance to trastuzumab and pertuzumab did not translate into differences in ER, PR, and HER2 receptor expression. In contrast, changes in the expression and activity of other HER family members, particularly HER4, were observed. In the same vein, analyses of the receptor and effector kinase status of different cellular pathways revealed that the MAPK pathway may be involved in the acquisition of resistance to trastuzumab and pertuzumab. Finally, proteomic analysis confirmed a significant change in the abundance patterns of more than 600 proteins with implications in key biological processes, such as ribosome formation, mitochondrial activity, and metabolism, which could be relevant mechanisms in the generation of resistance in HER2-positive breast cancer. We concluded that these resistant BCCLs may be a valuable tool to better understand the mechanisms of acquisition of resistance to trastuzumab and pertuzumab-based anti-HER2 therapy.
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Affiliation(s)
- Marta Sanz-Álvarez
- Department of Pathology, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain; (M.S.-Á.); (M.L.); (M.M.-G.)
| | - Melani Luque
- Department of Pathology, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain; (M.S.-Á.); (M.L.); (M.M.-G.)
| | - Miriam Morales-Gallego
- Department of Pathology, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain; (M.S.-Á.); (M.L.); (M.M.-G.)
| | - Ion Cristóbal
- Translational Oncology Division, OncoHealth Institute, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain;
| | | | - Yamileth Rangel
- Department of Pathology, Infanta Elena University Hospital, 28342 Madrid, Spain;
| | - Yann Izarzugaza
- Department of Medical Oncology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain;
| | - Pilar Eroles
- Institute of Health Research INCLIVA—CIBERONC, 46010 Valencia, Spain;
- Department of Physiology, University of Valencia, 46010 Valencia, Spain
| | - Joan Albanell
- Cancer Research Program, IMIM (Hospital del Mar Research Institute), 08003 Barcelona, Spain;
- Department of Medical Oncology, Hospital del Mar—CIBERONC, 08003 Barcelona, Spain
- Department of Experimental and Health Sciences, Faculty of Medicine, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Juan Madoz-Gúrpide
- Department of Pathology, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain; (M.S.-Á.); (M.L.); (M.M.-G.)
| | - Federico Rojo
- Department of Pathology, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS—FJD, UAM)—CIBERONC, 28040 Madrid, Spain; (M.S.-Á.); (M.L.); (M.M.-G.)
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6
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Li N, Liu Y. LARP7 upregulates SIRT1 deacetylase activity and inhibits Th1/Th17 cytokine response in psoriatic mice. Allergol Immunopathol (Madr) 2023; 51:16-22. [PMID: 37937491 DOI: 10.15586/aei.v51i6.959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/22/2023] [Indexed: 11/09/2023]
Abstract
OBJECTIVE To investigate the possible role of La ribonucleoprotein 7 (LARP7) in psoriasis through a mouse model and uncover its underlying mechanism. METHODS The back skin of C57BL/6 mice was smeared with IMquimod (IMQ) cream for 7 days to induce psoriasis. Immunoblot kit was used to detect the deacetylase activity of SIRT1 (member of sirtuin family). Hematoxylin and eosin staining was used to assess the degree of psoriasis in mouse. Flow cytometry assays were performed to confirm effects on Th1/Th17 cell differentiation. Enzyme-linked-immunosorbent serologic assays were used to detect the level of secreted cytokines. RESULTS LARP7 upregulated SIRT1 deacetylase activity. LARP7 alleviated psoriasis symptoms in mice by upregulating SIRT1 deacetylase activity. In addition, LARP7 regulated Th1/Th17 cell differentiation in psoriatic mice. We further found that LARP7 inhibited Th1/Th17 cytokine. CONCLUSION LARP7 upregulated SIRT1 activity and inhibited Th1/Th17 cytokine response in psoriatic mice.
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Affiliation(s)
- Na Li
- Department of Dermatology, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yulei Liu
- Department of Dermatology, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China;
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7
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Palumbo RJ, Hanes SD. Catalytic activity of the Bin3/MEPCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543302. [PMID: 37333392 PMCID: PMC10274667 DOI: 10.1101/2023.06.01.543302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Methylphosphate Capping Enzyme (MEPCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MEPCE in vitro, little is known about its functions in vivo, or what roles- if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MEPCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MEPCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MEPCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
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8
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Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn CD, Cheng X, Jiang YX, Zhou ZH, Feigon J. Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR. J Mol Biol 2023; 435:168044. [PMID: 37330293 PMCID: PMC10988774 DOI: 10.1016/j.jmb.2023.168044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains-N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65-TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65-TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65-TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.
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Affiliation(s)
- Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yao He
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yanjiao Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Mahavir Singh
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Xinyi Cheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yi Xiao Jiang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA.
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9
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Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR. 7SK methylation by METTL3 promotes transcriptional activity. SCIENCE ADVANCES 2023; 9:eade7500. [PMID: 37163588 PMCID: PMC10171809 DOI: 10.1126/sciadv.ade7500] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
A fundamental feature of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. The small nuclear RNA 7SK prevents transcriptional elongation by sequestering the cyclin dependent kinase 9/cyclin T1 (CDK9/CCNT1) positive transcription elongation factor (P-TEFb) complex. We found that epidermal growth factor signaling induces phosphorylation of the enzyme methyltransferase 3 (METTL3), leading to METTL3-mediated methylation of 7SK. 7SK methylation enhanced its binding to heterogeneous nuclear ribonucleoproteins, causing the release of the HEXIM1 P-TEFb complex subunit1 (HEXIM1)/P-TEFb complex and inducing transcriptional elongation. Our findings establish the mechanism underlying 7SK activation and uncover a previously unknown function for the m6A modification in converting growth factor signaling events into a regulatory transcriptional response via an RNA methylation-dependent switch.
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Affiliation(s)
- Marcelo Perez-Pepe
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Anthony W. Desotell
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hengyi Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Bing Han
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Daryl E. Klein
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudio R. Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
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10
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Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023; 10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
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Affiliation(s)
- Momodou B. Camara
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Amr M. Sobeh
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Catherine D. Eichhorn
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, United States
- *Correspondence: Catherine D. Eichhorn,
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11
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Ji C, Deng C, Antor K, Bischler T, Schneider C, Fischer U, Sendtner M, Briese M. hnRNP
R negatively regulates transcription by modulating the association of
P‐TEFb
with
7SK
and
BRD4. EMBO Rep 2022; 23:e55432. [PMID: 35856391 PMCID: PMC9442301 DOI: 10.15252/embr.202255432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Changhe Ji
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Chunchu Deng
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Katharina Antor
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine University of Wuerzburg Wuerzburg Germany
| | - Cornelius Schneider
- Department of Biochemistry, Theodor Boveri Institute University of Wuerzburg Wuerzburg Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute University of Wuerzburg Wuerzburg Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Michael Briese
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
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12
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Yang Y, Liu S, Egloff S, Eichhorn CD, Hadjian T, Zhen J, Kiss T, Zhou ZH, Feigon J. Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP. Mol Cell 2022; 82:1724-1736.e7. [PMID: 35320752 PMCID: PMC9081187 DOI: 10.1016/j.molcel.2022.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/27/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023]
Abstract
7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.
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Affiliation(s)
- Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvain Egloff
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tanya Hadjian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Zhen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamás Kiss
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; Biological Research Centre, Szeged, Temesvári krt. 62, 6726, Hungary
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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13
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Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022; 82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
Abstract
7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.
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Affiliation(s)
- Samuel W Olson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Anne-Marie W Turner
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Irfana Saleem
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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14
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The methyl phosphate capping enzyme Bmc1/Bin3 is a stable component of the fission yeast telomerase holoenzyme. Nat Commun 2022; 13:1277. [PMID: 35277511 PMCID: PMC8917221 DOI: 10.1038/s41467-022-28985-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
The telomerase holoenzyme is critical for maintaining eukaryotic genome integrity. In addition to a reverse transcriptase and an RNA template, telomerase contains additional proteins that protect the telomerase RNA and promote holoenzyme assembly. Here we report that the methyl phosphate capping enzyme (MePCE) Bmc1/Bin3 is a stable component of the S. pombe telomerase holoenzyme. Bmc1 associates with the telomerase holoenzyme and U6 snRNA through an interaction with the recently described LARP7 family member Pof8, and we demonstrate that these two factors are evolutionarily linked in fungi. Our data suggest that the association of Bmc1 with telomerase is independent of its methyltransferase activity, but rather that Bmc1 functions in telomerase holoenzyme assembly by promoting TER1 accumulation and Pof8 recruitment to TER1. Taken together, this work yields new insight into the composition, assembly, and regulation of the telomerase holoenzyme in fission yeast as well as the breadth of its evolutionary conservation.
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15
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Liang X, Wu S, Geng Z, Liu L, Zhang S, Wang S, Zhang Y, Huang Y, Zhang B. LARP7 Suppresses Endothelial-to-Mesenchymal Transition by Coupling With TRIM28. Circ Res 2021; 129:843-856. [PMID: 34503347 DOI: 10.1161/circresaha.121.319590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaodong Liang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
| | - Shuo Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
| | - Li Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
| | - Shiyan Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China (S. Wang)
| | - Yan Zhang
- Renji-Med Clinical Stem Cell Research Center, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, China (Y.Z.)
| | - Yu Huang
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China (Y.H.).,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China (Y.H.)
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, China (X.L., S. Wu, Z.G., L.L., S.Z., B.Z.)
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16
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Nguyen D, Buisine N, Fayol O, Michels AA, Bensaude O, Price DH, Uguen P. An alternative D. melanogaster 7SK snRNP. BMC Mol Cell Biol 2021; 22:43. [PMID: 34461828 PMCID: PMC8406779 DOI: 10.1186/s12860-021-00381-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The 7SK small nuclear RNA (snRNA) found in most metazoans is a key regulator of P-TEFb which in turn regulates RNA polymerase II elongation. Although its primary sequence varies in protostomes, its secondary structure and function are conserved across evolutionary distant taxa. RESULTS Here, we describe a novel ncRNA sharing many features characteristic of 7SK RNAs, in D. melanogaster. We examined the structure of the corresponding gene and determined the expression profiles of the encoded RNA, called snRNA:7SK:94F, during development. It is probably produced from the transcription of a lncRNA which is processed into a mature snRNA. We also addressed its biological function and we show that, like dm7SK, this alternative 7SK interacts in vivo with the different partners of the P-TEFb complex, i.e. HEXIM, LARP7 and Cyclin T. This novel RNA is widely expressed across tissues. CONCLUSION We propose that two distinct 7SK genes might contribute to the formation of the 7SK snRNP complex in D. melanogaster.
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Affiliation(s)
- Duy Nguyen
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France
| | | | - Olivier Fayol
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France
| | | | - Olivier Bensaude
- IBENS Paris, UMR CNRS 8197; UA INSERM 1024, 75005, Paris, France
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Patricia Uguen
- Université Paris-Saclay, INSERM, CNRS, Interactions cellulaires et physiopathologie hépatique, Bât.440, 91405, Orsay, France.
- Present address: Université Paris-Saclay, CNRS, INSERM, Institut Curie, Intégrité du Génome, ARN et cancer, Bât. 110, 91401, Orsay cedex, France.
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17
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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18
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Briese M, Sendtner M. Keeping the balance: The noncoding RNA 7SK as a master regulator for neuron development and function. Bioessays 2021; 43:e2100092. [PMID: 34050960 DOI: 10.1002/bies.202100092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022]
Abstract
The noncoding RNA 7SK is a critical regulator of transcription by adjusting the activity of the kinase complex P-TEFb. Release of P-TEFb from 7SK stimulates transcription at many genes by promoting productive elongation. Conversely, P-TEFb sequestration by 7SK inhibits transcription. Recent studies have shown that 7SK functions are particularly important for neuron development and maintenance and it can thus be hypothesized that 7SK is at the center of many signaling pathways contributing to neuron function. 7SK activates neuronal gene expression programs that are key for terminal differentiation of neurons. Proteomics studies revealed a complex protein interactome of 7SK that includes several RNA-binding proteins. Some of these novel 7SK subcomplexes exert non-canonical cytosolic functions in neurons by regulating axonal mRNA transport and fine-tuning spliceosome production in response to transcription alterations. Thus, a picture emerges according to which 7SK acts as a multi-functional RNA scaffold that is integral for neuron homeostasis.
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Affiliation(s)
- Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
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19
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Ji C, Bader J, Ramanathan P, Hennlein L, Meissner F, Jablonka S, Mann M, Fischer U, Sendtner M, Briese M. Interaction of 7SK with the Smn complex modulates snRNP production. Nat Commun 2021; 12:1278. [PMID: 33627647 PMCID: PMC7904863 DOI: 10.1038/s41467-021-21529-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/29/2021] [Indexed: 11/09/2022] Open
Abstract
Gene expression requires tight coordination of the molecular machineries that mediate transcription and splicing. While the interplay between transcription kinetics and spliceosome fidelity has been investigated before, less is known about mechanisms regulating the assembly of the spliceosomal machinery in response to transcription changes. Here, we report an association of the Smn complex, which mediates spliceosomal snRNP biogenesis, with the 7SK complex involved in transcriptional regulation. We found that Smn interacts with the 7SK core components Larp7 and Mepce and specifically associates with 7SK subcomplexes containing hnRNP R. The association between Smn and 7SK complexes is enhanced upon transcriptional inhibition leading to reduced production of snRNPs. Taken together, our findings reveal a functional association of Smn and 7SK complexes that is governed by global changes in transcription. Thus, in addition to its canonical nuclear role in transcriptional regulation, 7SK has cytosolic functions in fine-tuning spliceosome production according to transcriptional demand. The noncoding RNA 7SK controls the transcription of mRNAs. Here, the authors show that the 7SK complex interacts with the Smn complex, suggesting crosstalk between transcription and snRNP assembly.
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Affiliation(s)
- Changhe Ji
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jakob Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Pradhipa Ramanathan
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Luisa Hennlein
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department for Systems Immunology & Proteomics, Institute of Innate Immunity, University Hospitals, University of Bonn, Bonn, Germany
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
| | - Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
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20
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Basu R, Eichhorn CD, Cheng R, Peterson RD, Feigon J. Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins. RNA Biol 2020; 18:1181-1192. [PMID: 33131423 DOI: 10.1080/15476286.2020.1836891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein complex that maintains the telomeric DNA at eukaryotic chromosome ends. p65 is important for the ordered assembly of telomerase RNA (TER) with telomerase reverse transcriptase. Unexpectedly, Schizosaccharomyces pombe Pof8 was recently identified as a LARP7 protein and a core component of fission yeast telomerase essential for biogenesis. LARP7 proteins have a conserved N-terminal La motif and RRM1 (La module) and C-terminal RRM2 with specific RNA substrate recognition attributed to RRM2, first structurally characterized in p65 as an atypical RRM named xRRM. Here we present the X-ray crystal structure and NMR studies of S. pombe Pof8 RRM2. Sequence and structure comparison of Pof8 RRM2 to p65 and human Larp7 xRRMs reveals conserved features for RNA binding with the main variability in the length of the non-canonical helix α3. This study shows that Pof8 has conserved xRRM features, providing insight into TER recognition and the defining characteristics of the xRRM.
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Affiliation(s)
- Ritwika Basu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ryan Cheng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert D Peterson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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21
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Číž M, Dvořáková A, Skočková V, Kubala L. The Role of Dietary Phenolic Compounds in Epigenetic Modulation Involved in Inflammatory Processes. Antioxidants (Basel) 2020; 9:antiox9080691. [PMID: 32756302 PMCID: PMC7464822 DOI: 10.3390/antiox9080691] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 01/09/2023] Open
Abstract
A better understanding of the interactions between dietary phenolic compounds and the epigenetics of inflammation may impact pathological conditions and their treatment. Phenolic compounds are well-known for their antioxidant, anti-inflammatory, anti-angiogenic, and anti-cancer properties, with potential benefits in the treatment of various human diseases. Emerging studies bring evidence that nutrition may play an essential role in immune system modulation also by altering gene expression. This review discusses epigenetic mechanisms such as DNA methylation, post-translational histone modification, and non-coding microRNA activity that regulate the gene expression of molecules involved in inflammatory processes. Special attention is paid to the molecular basis of NF-κB modulation by dietary phenolic compounds. The regulation of histone acetyltransferase and histone deacetylase activity, which all influence NF-κB signaling, seems to be a crucial mechanism of the epigenetic control of inflammation by phenolic compounds. Moreover, chronic inflammatory processes are reported to be closely connected to the major stages of carcinogenesis and other non-communicable diseases. Therefore, dietary phenolic compounds-targeted epigenetics is becoming an attractive approach for disease prevention and intervention.
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Affiliation(s)
- Milan Číž
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (A.D.); (V.S.); (L.K.)
- Correspondence: ; Tel.: +420-541-517-104
| | - Adéla Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (A.D.); (V.S.); (L.K.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Veronika Skočková
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (A.D.); (V.S.); (L.K.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Lukáš Kubala
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (A.D.); (V.S.); (L.K.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
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22
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Täuber H, Hüttelmaier S, Köhn M. POLIII-derived non-coding RNAs acting as scaffolds and decoys. J Mol Cell Biol 2020; 11:880-885. [PMID: 31152666 PMCID: PMC6884708 DOI: 10.1093/jmcb/mjz049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/11/2019] [Accepted: 04/14/2019] [Indexed: 12/17/2022] Open
Abstract
A large variety of eukaryotic small structured POLIII-derived non-coding RNAs (ncRNAs) have been described in the past. However, for only few, e.g. 7SL and H1/MRP families, cellular functions are well understood. For the vast majority of these transcripts, cellular functions remain unknown. Recent findings on the role of Y RNAs and other POLIII-derived ncRNAs suggest an evolutionarily conserved function of these ncRNAs in the assembly and function of ribonucleoprotein complexes (RNPs). These RNPs provide cellular `machineries’, which are essential for guiding the fate and function of a variety of RNAs. In this review, we summarize current knowledge on the role of POLIII-derived ncRNAs in the assembly and function of RNPs. We propose that these ncRNAs serve as scaffolding factors that `chaperone’ RNA-binding proteins (RBPs) to form functional RNPs. In addition or associated with this role, some small ncRNAs act as molecular decoys impairing the RBP-guided control of RNA fate by competing with other RNA substrates. This suggests that POLIII-derived ncRNAs serve essential and conserved roles in the assembly of larger RNPs and thus the control of gene expression by indirectly guiding the fate of mRNAs and lncRNAs.
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Affiliation(s)
- Hendrik Täuber
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Marcel Köhn
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany.,Julius Bernstein Institute of Physiology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
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23
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Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1. Biomolecules 2020; 10:biom10060872. [PMID: 32517187 PMCID: PMC7356810 DOI: 10.3390/biom10060872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/31/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells determine the protein output of their genetic program by regulating mRNA transcription, localization, translation and turnover rates. This regulation is accomplished by an ensemble of RNA-binding proteins (RBPs) that bind to any given mRNA, thus forming mRNPs. Poly(A) binding proteins (PABPs) are prominent members of virtually all mRNPs that possess poly(A) tails. They serve as multifunctional scaffolds, allowing the recruitment of diverse factors containing a poly(A)-interacting motif (PAM) into mRNPs. We present the crystal structure of the variant PAM motif (termed PAM2w) in the N-terminal part of the positive translation factor LARP4B, which binds to the MLLE domain of the poly(A) binding protein C1 cytoplasmic 1 (PABPC1). The structural analysis, along with mutational studies in vitro and in vivo, uncovered a new mode of interaction between PAM2 motifs and MLLE domains.
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24
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Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
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25
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Röder K, Stirnemann G, Dock-Bregeon AC, Wales DJ, Pasquali S. Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding. Nucleic Acids Res 2020; 48:373-389. [PMID: 31732748 PMCID: PMC7145557 DOI: 10.1093/nar/gkz1071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 12/25/2022] Open
Abstract
7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation of transcription by RNA-polymerase II, via its interaction with the positive transcription elongation factor P-TEFb. The interaction is induced by binding of the protein HEXIM to the 5′ hairpin (HP1) of 7SK RNA. Four distinct structural models have been obtained experimentally for HP1. Here, we employ computational methods to investigate the relative stability of these structures, transitions between them, and the effects of mutations on the observed structural ensembles. We further analyse the results with respect to mutational binding assays, and hypothesize a mechanism for HEXIM binding. Our results indicate that the dominant structure in the wild type exhibits a triplet involving the unpaired nucleotide U40 and the base pair A43-U66 in the GAUC/GAUC repeat. This conformation leads to an open major groove with enough potential binding sites for peptide recognition. Sequence mutations of the RNA change the relative stability of the different structural ensembles. Binding affinity is consequently lost if these changes alter the dominant structure.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Anne-Catherine Dock-Bregeon
- Laboratoire de Biologie Intégrative des Modèles Marins, UMR CNRS 8227, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Samuela Pasquali
- Laboratoire CiTCoM, CNRS UMR 8038, Université de Paris, 4 Avenue de l'observatoire, 75270 Paris, France
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The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Mol Cell 2020; 77:1014-1031.e13. [DOI: 10.1016/j.molcel.2020.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/25/2019] [Accepted: 12/26/2019] [Indexed: 12/12/2022]
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Dock-Bregeon AC, Lewis KA, Conte MR. The La-related proteins: structures and interactions of a versatile superfamily of RNA-binding proteins. RNA Biol 2019; 18:178-193. [PMID: 31752575 DOI: 10.1080/15476286.2019.1695712] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The La-related proteins (LaRPs) are an ancient superfamily of RNA-binding proteins orchestrating the major fates of RNA, from processing and maturation to regulation of mRNA translation. LaRPs are instrumental in modulating complex assemblies where the RNA is bound, folded, processed, escorted and presented to the functional effectors often through recruitment of protein partners. This intricate web of protein-RNA and protein-protein interactions is enabled by the modular nature of the LaRPs, comprising several structured domains connected by flexible linkers, and other sequences lacking recognizable folded motifs. Recent structures, together with biochemical and biophysical studies, have provided insights into how each LaRP family has evolved unique mechanisms of RNA recognition, not only through the conserved RNA-binding unit, the La-module, but also mediated by other family-specific motifs. Furthermore, in a series of unexpected twists and turns, they have revealed that the dynamic and conformational interplay of multi-structured domains and disordered regions operate in unison to achieve RNA substrate discrimination. This review proposes a perspective of our current knowledge of the structure-function relationship of the LaRP superfamily.
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Affiliation(s)
| | - Karen A Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
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Schneeberger PE, Bierhals T, Neu A, Hempel M, Kutsche K. de novo MEPCE nonsense variant associated with a neurodevelopmental disorder causes disintegration of 7SK snRNP and enhanced RNA polymerase II activation. Sci Rep 2019; 9:12516. [PMID: 31467394 PMCID: PMC6715695 DOI: 10.1038/s41598-019-49032-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
In eukaryotes, the elongation phase of transcription by RNA polymerase II (RNAP II) is regulated by the transcription elongation factor b (P-TEFb), composed of Cyclin-T1 and cyclin-dependent kinase 9. The release of RNAP II is mediated by phosphorylation through P-TEFb that in turn is under control by the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. The 7SK snRNP consists of the 7SK non-coding RNA and the proteins MEPCE, LARP7, and HEXIM1/2. Biallelic LARP7 loss-of-function variants underlie Alazami syndrome characterized by growth retardation and intellectual disability. We report a boy with global developmental delay and seizures carrying the de novo MEPCE nonsense variant c.1552 C > T/p.(Arg518*). mRNA and protein analyses identified nonsense-mediated mRNA decay to underlie the decreased amount of MEPCE in patient fibroblasts followed by LARP7 and 7SK snRNA downregulation and HEXIM1 upregulation. Reduced binding of HEXIM1 to Cyclin-T1, hyperphosphorylation of the RNAP II C-terminal domain, and upregulated expression of ID2, ID3, MRPL11 and snRNAs U1, U2 and U4 in patient cells are suggestive of enhanced activation of P-TEFb. Flavopiridol treatment and ectopic MEPCE protein expression in patient fibroblasts rescued increased expression of six RNAP II-sensitive genes and suggested a possible repressive effect of MEPCE on P-TEFb-dependent transcription of specific genes.
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Affiliation(s)
- Pauline E Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Neu
- Childrens Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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29
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Von Dwingelo J, Chung IYW, Price CT, Li L, Jones S, Cygler M, Abu Kwaik Y. Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex. mBio 2019; 10:e01942-19. [PMID: 31455655 PMCID: PMC6712400 DOI: 10.1128/mbio.01942-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
Species of the Legionella genus encode at least 18,000 effector proteins that are translocated through the Dot/Icm type IVB translocation system into macrophages and protist hosts to enable intracellular growth. Eight effectors, including ankyrin H (AnkH), are common to all Legionella species. The AnkH effector is also present in Coxiella and Rickettsiella To date, no pathogenic effectors have ever been described that directly interfere with host cell transcription. We determined that the host nuclear protein La-related protein 7 (LARP7), which is a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, interacts with AnkH in the host cell nucleus. The AnkH-LARP7 interaction partially impedes interactions of the 7SK snRNP components with LARP7, interfering with transcriptional elongation by polymerase (Pol) II. Consistent with that, our data show AnkH-dependent global reprogramming of transcription of macrophages infected by Legionella pneumophila The crystal structure of AnkH shows that it contains four N-terminal ankyrin repeats, followed by a cysteine protease-like domain and an α-helical C-terminal domain. A substitution within the β-hairpin loop of the third ankyrin repeat results in diminishment of LARP7-AnkH interactions and phenocopies the ankH null mutant defect in intracellular growth. LARP7 knockdown partially suppresses intracellular proliferation of wild-type (WT) bacteria and increases the severity of the defect of the ΔankH mutant, indicating a role for LARP7 in permissiveness of host cells to intracellular bacterial infection. We conclude that the AnkH-LARP7 interaction impedes interaction of LARP7 with 7SK snRNP, which would block transcriptional elongation by Pol II, leading to host global transcriptional reprogramming and permissiveness to L. pneumophilaIMPORTANCE For intracellular pathogens to thrive in host cells, an environment that supports survival and replication needs to be established. L. pneumophila accomplishes this through the activity of the ∼330 effector proteins that are injected into host cells during infection. Effector functions range from hijacking host trafficking pathways to altering host cell machinery, resulting in altered cell biology and innate immunity. One such pathway is the host protein synthesis pathway. Five L. pneumophila effectors have been identified that alter host cell translation, and 2 effectors have been identified that indirectly affect host cell transcription. No pathogenic effectors have been described that directly interfere with host cell transcription. Here we show a direct interaction of the AnkH effector with a host cell transcription complex involved in transcriptional elongation. We identify a novel process by which AnkH interferes with host transcriptional elongation through interference with formation of a functional complex and show that this interference is required for pathogen proliferation.
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Affiliation(s)
- Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christopher T Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Lei Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Snake Jones
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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30
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Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M. P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress. Mol Cell 2019; 74:254-267.e10. [PMID: 30824372 PMCID: PMC6482433 DOI: 10.1016/j.molcel.2019.01.033] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/27/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38MAPK, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.
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Affiliation(s)
- Andrii Bugai
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki 00014, Finland
| | - Alexandre J C Quaresma
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki 00014, Finland
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Tina Lenasi
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki 00014, Finland
| | - Robert Düster
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Christopher R Sibley
- Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK; MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Koh Fujinaga
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Petra Kukanja
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki 00014, Finland
| | - Thomas Hennig
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Melanie Blasius
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Jernej Ule
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Neurology, University College London, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki 00014, Finland.
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31
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Yang Y, Eichhorn CD, Wang Y, Cascio D, Feigon J. Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE. Nat Chem Biol 2019; 15:132-140. [PMID: 30559425 PMCID: PMC6339579 DOI: 10.1038/s41589-018-0188-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023]
Abstract
Among RNA 5'-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second nonenzymatic role as a core component of the 7SK ribonuclear protein (RNP), an essential regulator of RNA transcription. We report 2.0- and 2.1-Å X-ray crystal structures of the human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5'-hairpin-single-stranded RNA region, thus explaining MePCE's specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition-state geometry. Unexpectedly, binding experiments showed that MePCE has higher affinity for capped versus uncapped 7SK, and kinetic data support a model of slow product release. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.
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Affiliation(s)
- Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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32
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Eichhorn CD, Yang Y, Repeta L, Feigon J. Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7. Proc Natl Acad Sci U S A 2018; 115:E6457-E6466. [PMID: 29946027 PMCID: PMC6048529 DOI: 10.1073/pnas.1806276115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The La and the La-related protein (LARP) superfamily is a diverse class of RNA binding proteins involved in RNA processing, folding, and function. Larp7 binds to the abundant long noncoding 7SK RNA and is required for 7SK ribonucleoprotein (RNP) assembly and function. The 7SK RNP sequesters a pool of the positive transcription elongation factor b (P-TEFb) in an inactive state; on release, P-TEFb phosphorylates RNA Polymerase II to stimulate transcription elongation. Despite its essential role in transcription, limited structural information is available for the 7SK RNP, particularly for protein-RNA interactions. Larp7 contains an N-terminal La module that binds UUU-3'OH and a C-terminal atypical RNA recognition motif (xRRM) required for specific binding to 7SK and P-TEFb assembly. Deletion of the xRRM is linked to gastric cancer in humans. We report the 2.2-Å X-ray crystal structure of the human La-related protein group 7 (hLarp7) xRRM bound to the 7SK stem-loop 4, revealing a unique binding interface. Contributions of observed interactions to binding affinity were investigated by mutagenesis and isothermal titration calorimetry. NMR 13C spin relaxation data and comparison of free xRRM, RNA, and xRRM-RNA structures show that the xRRM is preordered to bind a flexible loop 4. Combining structures of the hLarp7 La module and the xRRM-7SK complex presented here, we propose a structural model for Larp7 binding to the 7SK 3' end and mechanism for 7SK RNP assembly. This work provides insight into how this domain contributes to 7SK recognition and assembly of the core 7SK RNP.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Lucas Repeta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
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Abstract
BACKGROUND The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell. The virus will either actively replicate to promote dissemination in blood and tissues, or become dormant mostly in memory CD4+ T cells, as part of a small but long-living latent reservoir, the main obstacle for HIV eradication. OBJECTIVE In this review, we summarize recent advances in the understanding of the multi-step mechanism that regulates Tat-mediated HIV-1 transcription and RNA polymerase II release, to promote viral transcription elongation. Early events of the human transcription elongation factor b release from the inhibitory 7SK small nuclear ribonucleoprotein complex and its recruitment to the HIV promoter will be discussed. Specific roles of the super elongation complex subunits during transcription elongation, and insight on recently identified cellular factors and mechanisms regulating HIV latency will be detailed. CONCLUSION Understanding the complexity of HIV transcriptional regulation by host factors may open the door for development of novel strategies to eradicate the resilient latent reservoir.
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Affiliation(s)
- Guillaume Mousseau
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| | - Susana T Valente
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
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34
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Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
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35
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Funakoshi M, Tsuda M, Muramatsu K, Hatsuda H, Morishita S, Aigaki T. Overexpression of Larp4B downregulates dMyc and reduces cell and organ sizes in Drosophila. Biochem Biophys Res Commun 2018; 497:762-768. [PMID: 29462618 DOI: 10.1016/j.bbrc.2018.02.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 11/27/2022]
Abstract
Regulation of cell and organ sizes is fundamental for all organisms, but its molecular basis is not fully understood. Here we performed a gain-of-function screen and identified larp4B whose overexpression reduces cell and organ sizes in Drosophila melanogaster. Larp4B is a member of La-related proteins (LARPs) containing an LA motif and an adjacent RNA recognition motif (RRM), and play diverse roles in RNA metabolism. However, the function of Larp4B has remained poorly characterized. We generated transgenic flies overexpressing wild-type Larp4B or a deletion variant lacking the LA and RRM domains, and demonstrated that the RNA-binding domains are essential for Larp4B to reduce cell and organ sizes. We found that the larp4B-induced phenotype was suppressed by dMyc overexpression, which promotes cell growth and survival. Furthermore, overexpression of larp4B decreased dMyc protein levels, whereas its loss-of-function mutation had an opposite effect. Our results suggest that Larp4B is a negative regulator of dMyc.
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Affiliation(s)
- Masabumi Funakoshi
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji-shi, Tokyo 192-0397, Japan
| | - Manabu Tsuda
- Department of Liberal Arts and Human Development, Kanagawa University of Human Services, 1-10-1, Heiseicho, Yokosuka-shi, Kanagawa 238-8522, Japan
| | - Keigo Muramatsu
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Hatsuda
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-0882, Japan
| | - Shinichi Morishita
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-0882, Japan
| | - Toshiro Aigaki
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji-shi, Tokyo 192-0397, Japan.
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36
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Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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37
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Brogie JE, Price DH. Reconstitution of a functional 7SK snRNP. Nucleic Acids Res 2017; 45:6864-6880. [PMID: 28431135 PMCID: PMC5499737 DOI: 10.1093/nar/gkx262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 01/29/2023] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro. Stably associated P-TEFb was highly inhibited, but could still be released and activated by HIV-1 Tat. Notably, P-TEFb association with both in vitro-reconstituted and cellular snRNPs led to similar changes in SHAPE reactivities, confirming that 7SK undergoes a P-TEFb-dependent structural change. We determined that the xRRM of LARP7 binds to the 3΄ stem loop of 7SK and inhibits the methyltransferase activity of MEPCE through a C-terminal MEPCE interaction domain (MID). Inhibition of MEPCE is dependent on the structure of the 3΄ stem loop and the closed form of 7SK RNA. This study provides important insights into intramolecular interactions within the 7SK snRNP.
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Affiliation(s)
- John E Brogie
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
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38
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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Martinez-Zapien D, Legrand P, McEwen AG, Proux F, Cragnolini T, Pasquali S, Dock-Bregeon AC. The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK. Nucleic Acids Res 2017; 45:3568-3579. [PMID: 28082395 PMCID: PMC5389472 DOI: 10.1093/nar/gkw1351] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022] Open
Abstract
In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation factor P-TEFb and prevents phosphorylation of pausing factors. The HEXIM-binding site embedded in the 5΄-hairpin of 7SK (HP1) encompasses a short signature sequence, a GAUC repeat framed by single-stranded uridines. The present crystal structure of HP1 shows a remarkably straight helical stack involving several unexpected triples formed at a central region. Surprisingly, two uridines of the signature sequence make triple interactions in the major groove of the (GAUC)2. The third uridine is turned outwards or inward, wedging between the other uridines, thus filling the major groove. A molecular dynamics simulation indicates that these two conformations of the signature sequence represent stable alternatives. Analyses of the interaction with the HEXIM protein confirm the importance of the triple interactions at the signature sequence. Altogether, the present structural analysis of 7SK HP1 highlights an original mechanism of swapping bases, which could represent a possible ‘7SK signature’ and provides new insight into the functional importance of the plasticity of RNA.
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Affiliation(s)
- Denise Martinez-Zapien
- Biotechnologie et signalisation cellulaire, CNRS UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, F-91190 Gif-sur-Yvette, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Florence Proux
- Department of functional genomics, CNRS UMR 8197, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Department of functional genomics, INSERM-U1024, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France
| | | | - Samuela Pasquali
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR 9080, Université Sorbonne Paris Cite, Paris Diderot, 75005 Paris, France
| | - Anne-Catherine Dock-Bregeon
- Department of functional genomics, CNRS UMR 8197, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Department of functional genomics, INSERM-U1024, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Sorbonne Universités UPMC, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
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40
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Egloff S, Vitali P, Tellier M, Raffel R, Murphy S, Kiss T. The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression. EMBO J 2017; 36:934-948. [PMID: 28254838 DOI: 10.15252/embj.201695740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 11/09/2022] Open
Abstract
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes. The 7SK snRNA specifically associates with a fraction of RNAPII hyperphosphorylated at Ser5 and Ser7, which is a hallmark of RNAPII engaged in snRNA synthesis. Chromatin immunoprecipitation (ChIP) and chromatin isolation by RNA purification (ChIRP) experiments revealed enrichments for all components of the 7SK snRNP on RNAPII-specific sn/snoRNA genes. Depletion of 7SK snRNA or Larp7 disrupts LEC integrity, inhibits RNAPII recruitment to RNAPII-specific sn/snoRNA genes, and reduces nascent snRNA and snoRNA synthesis. Thus, through controlling both mRNA elongation and sn/snoRNA synthesis, the 7SK snRNP is a key regulator of nuclear RNA production by RNAPII.
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Affiliation(s)
- Sylvain Egloff
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Patrice Vitali
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Raoul Raffel
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France .,Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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41
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Bourbigot S, Dock-Bregeon AC, Eberling P, Coutant J, Kieffer B, Lebars I. Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA. RNA (NEW YORK, N.Y.) 2016; 22:1844-1858. [PMID: 27852926 PMCID: PMC5113205 DOI: 10.1261/rna.056523.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/10/2016] [Indexed: 05/10/2023]
Abstract
The small nuclear 7SK RNA regulates RNA polymerase II (RNA Pol II) transcription, by sequestering and inhibiting the positive transcription elongation factor b (P-TEFb). P-TEFb is stored in the 7SK ribonucleoprotein (RNP) that contains the three nuclear proteins Hexim1, LaRP7, and MePCE. P-TEFb interacts with the protein Hexim1 and the 7SK RNA. Once P-TEFb is released from the 7SK RNP, it activates transcription by phosphorylating the C-terminal domain of RNA Pol II. P-TEFb also plays a crucial role in the replication of the human immunodeficiency virus HIV-1, through its recruitment by the viral transactivator Tat. Previous work demonstrated that the protein Tat promotes the release of P-TEFb from the 7SK RNP through direct binding to the 7SK RNA. Hexim1 and Tat proteins both comprise conserved and similar arginine-rich motifs that were identified to bind the 7SK RNA at a repeated GAUC site located at the top of the 5'-terminal hairpin (HPI). Here, we report the solution structure of this region as determined by nuclear magnetic resonance, to identify HPI structural features recognized by Hexim1 and Tat. The HPI solution structure displays an elongated shape featuring four helical segments interrupted by one internal loop and three bulges with distinct folds. In particular, the repeated GAUC motif adopts a pre-organized geometry. Our results suggest that the binding of Hexim1 and Tat to the 7SK RNA could originate from a conformational selection of this motif, highlighting how RNA local structure could lead to an adaptive recognition of their partners.
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Affiliation(s)
- Sarah Bourbigot
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Anne-Catherine Dock-Bregeon
- Department of Functional Genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 75005 Paris, France
| | - Pascal Eberling
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Jérôme Coutant
- Bruker BioSpin SAS, BP 10002, 67166 Wissembourg Cedex, France
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Isabelle Lebars
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
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42
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Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
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43
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C Quaresma AJ, Bugai A, Barboric M. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res 2016; 44:7527-39. [PMID: 27369380 PMCID: PMC5027500 DOI: 10.1093/nar/gkw585] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023] Open
Abstract
Release of RNA polymerase II (Pol II) from promoter-proximal pausing has emerged as a critical step regulating gene expression in multicellular organisms. The transition of Pol II into productive elongation requires the kinase activity of positive transcription elongation factor b (P-TEFb), which is itself under a stringent control by the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Here, we provide an overview on stimulating Pol II pause release by P-TEFb and on sequestering P-TEFb into 7SK snRNP. Furthermore, we highlight mechanisms that govern anchoring of 7SK snRNP to chromatin as well as means that release P-TEFb from the inhibitory complex, and propose a unifying model of P-TEFb activation on chromatin. Collectively, these studies shine a spotlight on the central role of RNA binding proteins (RBPs) in directing the inhibition and activation of P-TEFb, providing a compelling paradigm for controlling Pol II transcription with a non-coding RNA.
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Affiliation(s)
- Alexandre J C Quaresma
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Andrii Bugai
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Matjaz Barboric
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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44
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McNamara RP, Bacon CW, D'Orso I. Transcription elongation control by the 7SK snRNP complex: Releasing the pause. Cell Cycle 2016; 15:2115-2123. [PMID: 27152730 DOI: 10.1080/15384101.2016.1181241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability for the eukaryotic cell to transcriptionally respond to various stimuli is critical for the overall homeostasis of the cell, and in turn, the organism. The human RNA polymerase II complex (Pol II), which is responsible for the transcription of protein-encoding genes and non-coding RNAs, is paused at promoter-proximal regions to ensure their rapid activation. In response to stimulation, Pol II pause release is facilitated by the action of positive transcription elongation factors such as the P-TEFb kinase. However, the majority of P-TEFb is held in a catalytically inactivate state, assembled into the 7SK small nuclear ribonucleoprotein (snRNP) complex, and must be dislodged to become catalytically active. In this review, we discuss mechanisms of 7SK snRNP recruitment to promoter-proximal regions and P-TEFb disassembly from the inhibitory snRNP to regulate 'on site' kinase activation and Pol II pause release.
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Affiliation(s)
- Ryan P McNamara
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Curtis W Bacon
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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45
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Abstract
RNA polymerase II (Pol II) pausing at promoter-proximal regions is a highly regulated step in the transcription cycle. Pause release is facilitated by the P-TEFb kinase, which phosphorylates Pol II and negative elongation factors. Recent studies suggest that P-TEFb (as part of the inhibitory 7SK snRNP) is recruited to promoter-proximal regions through interaction with KAP1/TRIM28/TIF1β to facilitate 'on-site' kinase activation and transcription elongation. Here, I discuss features of this model and future challenges to further hone our understanding of transcriptional regulation including Pol II pausing and pause release.
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Affiliation(s)
- Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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46
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Slomnicki LP, Malinowska A, Kistowski M, Palusinski A, Zheng JJ, Sepp M, Timmusk T, Dadlez M, Hetman M. Nucleolar Enrichment of Brain Proteins with Critical Roles in Human Neurodevelopment. Mol Cell Proteomics 2016; 15:2055-75. [PMID: 27053602 DOI: 10.1074/mcp.m115.051920] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 11/06/2022] Open
Abstract
To study nucleolar involvement in brain development, the nuclear and nucleolar proteomes from the rat cerebral cortex at postnatal day 7 were analyzed using LC-MS/iTRAQ methodology. Data of the analysis are available via ProteomeXchange with identifier PXD002188. Among 504 candidate nucleolar proteins, the overrepresented gene ontology terms included such cellular compartmentcategories as "nucleolus", "ribosome" and "chromatin". Consistent with such classification, the most overrepresented functional gene ontology terms were related to RNA metabolism/ribosomal biogenesis, translation, and chromatin organization. Sixteen putative nucleolar proteins were associated with neurodevelopmental phenotypes in humans. Microcephaly and/or cognitive impairment were the most common phenotypic manifestations. Although several such proteins have links to ribosomal biogenesis and/or genomic stability/chromatin structure (e.g. EMG1, RPL10, DKC1, EIF4A3, FLNA, SMC1, ATRX, MCM4, NSD1, LMNA, or CUL4B), others including ADAR, LARP7, GTF2I, or TCF4 have no such connections known. Although neither the Alazami syndrome-associated LARP7nor the Pitt-Hopkins syndrome-associated TCF4 were reported in nucleoli of non-neural cells, in neurons, their nucleolar localization was confirmed by immunostaining. In cultured rat hippocampal neurons, knockdown of LARP7 reduced both perikaryal ribosome content and general protein synthesis. Similar anti-ribosomal/anti-translation effects were observed after knockdown of the ribosomal biogenesis factor EMG1 whose deficiency underlies Bowen-Conradi syndrome. Finally, moderate reduction of ribosome content and general protein synthesis followed overexpression of two Pitt-Hopkins syndrome mutant variants of TCF4. Therefore, dysregulation of ribosomal biogenesis and/or other functions of the nucleolus may disrupt neurodevelopment resulting in such phenotypes as microcephaly and/or cognitive impairment.
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Affiliation(s)
- Lukasz P Slomnicki
- From the ‡Kentucky Spinal Cord Injury Research Center and the Departments of Neurological Surgery and
| | - Agata Malinowska
- ¶Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michal Kistowski
- ¶Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Antoni Palusinski
- ‖Department of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jing-Juan Zheng
- From the ‡Kentucky Spinal Cord Injury Research Center and the Departments of Neurological Surgery and
| | - Mari Sepp
- **Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Tonis Timmusk
- **Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Michal Dadlez
- ¶Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michal Hetman
- From the ‡Kentucky Spinal Cord Injury Research Center and the Departments of Neurological Surgery and §Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky;
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47
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Gudipaty SA, D’Orso I. Functional interplay between PPM1G and the transcription elongation machinery. RNA & DISEASE 2016; 3:e1215. [PMID: 27088130 PMCID: PMC4830430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transcription elongation is a critical regulatory step in the gene expression cycle. One key regulator of the switch between transcription initiation and elongation is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) and several negative elongation factors to relieve the elongation block at paused promoters to facilitate productive elongation. Here, we highlight recent findings signifying the role of the PPM1G/PP2Cγ phosphatase in activating and maintaining the active transcription elongation state by regulating the availability of P-TEFb and blocking its assembly into the catalytic inactive 7SK small nuclear ribonucleoprotein (snRNP) complex.
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Affiliation(s)
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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48
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Gudipaty SA, McNamara RP, Morton EL, D'Orso I. PPM1G Binds 7SK RNA and Hexim1 To Block P-TEFb Assembly into the 7SK snRNP and Sustain Transcription Elongation. Mol Cell Biol 2015; 35:3810-28. [PMID: 26324325 PMCID: PMC4609742 DOI: 10.1128/mcb.00226-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/11/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022] Open
Abstract
Transcription elongation programs are vital for the precise regulation of several biological processes. One key regulator of such programs is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) once released from the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. Although mechanisms of P-TEFb release from the snRNP are becoming clearer, how P-TEFb remains in the 7SK-unbound state to sustain transcription elongation programs remains unknown. Here we report that the PPM1G phosphatase (inducibly recruited by nuclear factor κB [NF-κB] to target promoters) directly binds 7SK RNA and the kinase inhibitor Hexim1 once P-TEFb has been released from the 7SK snRNP. This dual binding activity of PPM1G blocks P-TEFb reassembly onto the snRNP to sustain NF-κB-mediated Pol II transcription in response to DNA damage. Notably, the PPM1G-7SK RNA interaction is direct, kinetically follows the recruitment of PPM1G to promoters to activate NF-κB transcription, and is reversible, since the complex disassembles before resolution of the program. Strikingly, we found that the ataxia telangiectasia mutated (ATM) kinase regulates the interaction between PPM1G and the 7SK snRNP through site-specific PPM1G phosphorylation. The precise and temporally regulated interaction of a cellular enzyme and a noncoding RNA provides a new paradigm for simultaneously controlling the activation and maintenance of inducible transcription elongation programs.
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Affiliation(s)
- Swapna Aravind Gudipaty
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ryan P McNamara
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Emily L Morton
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules 2015; 5:2701-22. [PMID: 26501340 PMCID: PMC4693254 DOI: 10.3390/biom5042701] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Abstract
The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.
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Affiliation(s)
- Chara Stavraka
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
| | - Sarah Blagden
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
- Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LE, UK.
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50
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Martinez-Zapien D, Saliou JM, Han X, Atmanene C, Proux F, Cianférani S, Dock-Bregeon AC. Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective. Biochimie 2015; 117:63-71. [PMID: 25863285 DOI: 10.1016/j.biochi.2015.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/25/2015] [Indexed: 11/18/2022]
Abstract
A 7SKsnRNP complex, comprising the non-coding RNA 7SK and proteins MePCE and LARP7, participates in the regulation of the transcription elongation by RNA-polymerase II in higher eukaryotes. Binding of a HEXIM protein triggers the inhibition of the kinase complex P-TEFb, a key actor of the switch from paused transcription to elongation. The present paper reviews what is known about the specific recognition of the 7SK RNA by the HEXIM protein. HEXIM uses an arginine-rich motif (ARM) peptide to bind one specific site in the 5'-hairpin of the 7SK RNA. Since HEXIM forms a dimer, what happens with the second ARM impacts the assembly symmetry. In order to help sort through possible models, a combination of native mass spectrometry and electrophoretic mobility shift assays was used. It provides evidence that only one ARM of the HEXIM dimer is directly binding to the RNA hairpin and that another sequence downstream of the ARM participates in a second binding event allowing the other monomer of HEXIM to bind the RNA.
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Affiliation(s)
- Denise Martinez-Zapien
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), Institute of Genetics and of Molecular and Cellular Biology (IGBMC) 67404 Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France; Biotechnologie et Signalisation Cellulaire UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch, France.
| | - Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France; Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, CNRS UMR 8204, INSERM U1019, Université Lille Nord de France, 1 rue du Pr. Calmette, 59000 Lille, France.
| | - Xiao Han
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France; Key Laboratory of Brain Functional Genomics, East China Normal University (ECNU), Shanghai, PR China.
| | - Cedric Atmanene
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France.
| | - Florence Proux
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France.
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France.
| | - Anne-Catherine Dock-Bregeon
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France.
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