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Abascal-Palacios G, Jochem L, Pla-Prats C, Beuron F, Vannini A. Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes. Nat Commun 2021; 12:6992. [PMID: 34848735 PMCID: PMC8632968 DOI: 10.1038/s41467-021-27338-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Here we present the cryo-EM reconstruction at 4.0 Å of an active Ty3 strand transfer complex bound to TFIIIB transcription factor and a tRNA gene. The structure unravels the molecular mechanisms underlying Ty3 targeting specificity at Pol III-transcribed genes and sheds light into the architecture of retrotransposon machinery during integration. Ty3 intasome contacts a region of TBP, a subunit of TFIIIB, which is blocked by NC2 transcription regulator in RNA Pol II-transcribed genes. A newly-identified chromodomain on Ty3 integrase interacts with TFIIIB and the tRNA gene, defining with extreme precision the integration site position.
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Affiliation(s)
| | - Laura Jochem
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Carlos Pla-Prats
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Human Technopole, 20157, Milan, Italy.
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Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
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Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Abstract
Transcription initiation is one of the key regulatory steps in expressing the genetic information encoded in the DNA . Mechanisms of RNA Pol II transcription have been extensively studied, whereas the structural basis of RNA Pol I and III transcription is still poorly defined. Three recent studies discussed here give a first glimpse into the molecular mechanisms underlying the process of RNA Pol I transcriptional initiation and reveal unexpected structural differences compared to the previously described homologous Pol II structures.
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