ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts
Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. R...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Cell and Developmental Biology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcell.2022.1080626/full |
| _version_ | 1828070504310767616 |
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| author | Riccardo Pecori Riccardo Pecori Isabel Chillón Claudio Lo Giudice Annette Arnold Sandra Wüst Marco Binder Marco Marcia Ernesto Picardi Fotini Nina Papavasiliou |
| author_facet | Riccardo Pecori Riccardo Pecori Isabel Chillón Claudio Lo Giudice Annette Arnold Sandra Wüst Marco Binder Marco Marcia Ernesto Picardi Fotini Nina Papavasiliou |
| author_sort | Riccardo Pecori |
| collection | DOAJ |
| description | Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events. |
| first_indexed | 2024-04-11T00:37:41Z |
| format | Article |
| id | doaj.art-0a436a508c1a41ffa1230acaf8099786 |
| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-04-11T00:37:41Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj.art-0a436a508c1a41ffa1230acaf80997862023-01-06T13:46:16ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2023-01-011010.3389/fcell.2022.10806261080626ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcriptsRiccardo Pecori0Riccardo Pecori1Isabel Chillón2Claudio Lo Giudice3Annette Arnold4Sandra Wüst5Marco Binder6Marco Marcia7Ernesto Picardi8Fotini Nina Papavasiliou9Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, GermanyHelmholtz Institute for Translational Oncology (HI-TRON), Mainz, GermanyEuropean Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, FranceDepartment of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, ItalyDivision of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, GermanyResearch Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, GermanyResearch Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, GermanyEuropean Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, FranceDepartment of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, ItalyDivision of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, GermanyDespite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events.https://www.frontiersin.org/articles/10.3389/fcell.2022.1080626/fullADARRNA editingU-to-CMultiEditRDDX58/RIG-ILINC-P21 |
| spellingShingle | Riccardo Pecori Riccardo Pecori Isabel Chillón Claudio Lo Giudice Annette Arnold Sandra Wüst Marco Binder Marco Marcia Ernesto Picardi Fotini Nina Papavasiliou ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts Frontiers in Cell and Developmental Biology ADAR RNA editing U-to-C MultiEditR DDX58/RIG-I LINC-P21 |
| title | ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts |
| title_full | ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts |
| title_fullStr | ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts |
| title_full_unstemmed | ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts |
| title_short | ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts |
| title_sort | adar rna editing on antisense rnas results in apparent u to c base changes on overlapping sense transcripts |
| topic | ADAR RNA editing U-to-C MultiEditR DDX58/RIG-I LINC-P21 |
| url | https://www.frontiersin.org/articles/10.3389/fcell.2022.1080626/full |
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