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Chédin F, Hartono SR, Sanz LA, Vanoosthuyse V. Best practices for the visualization, mapping, and manipulation of R-loops. EMBO J 2021; 40:e106394. [PMID: 33411340 PMCID: PMC7883053 DOI: 10.15252/embj.2020106394] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023] Open
Abstract
R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R-loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.
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Affiliation(s)
- Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la CelluleCNRSUMR 5239Univ LyonÉcole Normale Supérieure de LyonLyonFrance
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Storci G, Bacalini MG, Bonifazi F, Garagnani P, De Carolis S, Salvioli S, Olivieri F, Bonafè M. Ribosomal DNA instability: An evolutionary conserved fuel for inflammaging. Ageing Res Rev 2020; 58:101018. [PMID: 31926964 DOI: 10.1016/j.arr.2020.101018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/07/2019] [Accepted: 01/08/2020] [Indexed: 02/07/2023]
Abstract
Across eukaryotes, ribosomal DNA (rDNA) loci are characterized by intrinsic genomic instability due to their repetitive nature and their base composition that facilitate DNA double strand breaks and RNA:DNA hybrids formation. In the yeast, ribosomal DNA instability affects lifespan via the formation of extrachromosomal rDNA circles (ERC) that accrue into aged cells. In humans, rDNA instability has long been reported in a variety of progeric syndromes caused by the dysfunction of DNA helicases, but its role in physiological aging and longevity still needs to be clarified. Here we propose that rDNA instability leads to the activation of innate immunity and inflammation via the interaction with the cytoplasmic DNA sensing machinery. Owing to the recent clarified role of cytoplasmic DNA in the pro-inflammatory phenotype of senescent cells, we hypothesize that the accrual of rDNA derived molecules (i.e. ERC and RNA:DNA hybrids) may have a role in aging by contributing to inflammaging i.e. the systemic pro-inflammatory drift that associates with the onset of geriatric syndromes and age related dysfunctions in humans.
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Affiliation(s)
- Gianluca Storci
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy.
| | | | - Francesca Bonifazi
- Institute of Hematology "L. and A. Seràgnoli", University Hospital S. Orsola-Malpighi, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Sabrina De Carolis
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy; Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA National Institute, Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy.
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