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Wang Y, Traugot CM, Bubenik JL, Li T, Sheng P, Hiers NM, Fernandez P, Li L, Bian J, Swanson MS, Xie M. N 6-methyladenosine in 7SK small nuclear RNA underlies RNA polymerase II transcription regulation. Mol Cell 2023; 83:3818-3834.e7. [PMID: 37820733 PMCID: PMC10873123 DOI: 10.1016/j.molcel.2023.09.020] [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: 02/27/2023] [Revised: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
N6-methyladenosine (m6A) modifications play crucial roles in RNA metabolism. How m6A regulates RNA polymerase II (RNA Pol II) transcription remains unclear. We find that 7SK small nuclear RNA (snRNA), a regulator of RNA Pol II promoter-proximal pausing, is highly m6A-modified in non-small cell lung cancer (NSCLC) cells. In A549 cells, we identified eight m6A sites on 7SK and discovered methyltransferase-like 3 (METTL3) and alkB homolog 5 (ALKBH5) as the responsible writer and eraser. When the m6A-7SK is specifically erased by a dCasRx-ALKBH5 fusion protein, A549 cell growth is attenuated due to reduction of RNA Pol II transcription. Mechanistically, removal of m6A leads to 7SK structural rearrangements that facilitate sequestration of the positive transcription elongation factor b (P-TEFb) complex, which results in reduction of serine 2 phosphorylation (Ser2P) in the RNA Pol II C-terminal domain and accumulation of RNA Pol II in the promoter-proximal region. Taken together, we uncover that m6A modifications of a non-coding RNA regulate RNA Pol II transcription and NSCLC tumorigenesis.
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Affiliation(s)
- Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Jodi L Bubenik
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Paul Fernandez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Jiang Bian
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Health Outcomes & Biomedical Informatics, University of Florida, Gainesville, FL 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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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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Schärfen L, Neugebauer KM. Transcription Regulation Through Nascent RNA Folding. J Mol Biol 2021; 433:166975. [PMID: 33811916 DOI: 10.1016/j.jmb.2021.166975] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
Folding of RNA into secondary structures through intramolecular base pairing determines an RNA's three-dimensional architecture and associated function. Simple RNA structures like stem loops can provide specialized functions independent of coding capacity, such as protein binding, regulation of RNA processing and stability, stimulation or inhibition of translation. RNA catalysis is dependent on tertiary structures found in the ribosome, tRNAs and group I and II introns. While the extent to which non-coding RNAs contribute to cellular maintenance is generally appreciated, the fact that both non-coding and coding RNA can assume relevant structural states has only recently gained attention. In particular, the co-transcriptional folding of nascent RNA of all classes has the potential to regulate co-transcriptional processing, RNP (ribonucleoprotein particle) formation, and transcription itself. Riboswitches are established examples of co-transcriptionally folded coding RNAs that directly regulate transcription, mainly in prokaryotes. Here we discuss recent studies in both prokaryotes and eukaryotes showing that structure formation may carry a more widespread regulatory logic during RNA synthesis. Local structures forming close to the catalytic center of RNA polymerases have the potential to regulate transcription by reducing backtracking. In addition, stem loops or more complex structures may alter co-transcriptional RNA processing or its efficiency. Several examples of functional structures have been identified to date, and this review provides an overview of physiologically distinct processes where co-transcriptionally folded RNA plays a role. Experimental approaches such as single-molecule FRET and in vivo structural probing to further advance our insight into the significance of co-transcriptional structure formation are discussed.
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Affiliation(s)
- Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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