Exploring RNA modifications in infectious non-coding circular RNAs
Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explor...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-02-01
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| Series: | RNA Biology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/15476286.2025.2459039 |
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| author | Pavel Vopalensky Anton Škríba Michela Chiumenti Lucia Ďuričeková Anna Šimonová Ondřej Lukšan Francesco di Serio Beatriz Navarro Hana Cahova |
| author_facet | Pavel Vopalensky Anton Škríba Michela Chiumenti Lucia Ďuričeková Anna Šimonová Ondřej Lukšan Francesco di Serio Beatriz Navarro Hana Cahova |
| author_sort | Pavel Vopalensky |
| collection | DOAJ |
| description | Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC – MS and Oxford Nanopore Technology (ONT) direct RNA sequencing. Although no modification was detected in ASBVd, CEVd contained approximately one m6A per RNA molecule. ONT sequencing predicted three m6A positions. Employing orthogonal SELECT method, we confirmed m6A in two positions A353 and A360, which are highly conserved among CEVd variants. These positions are located in the left terminal region of the CEVd rod-like structure where likely RNA Pol II and and TFIIIA-7ZF bind, thus suggesting potential biological role of methylation in viroid replication. |
| format | Article |
| id | doaj-art-a2b1d585a5ed49e18c68f69cffcd521e |
| institution | Kabale University |
| issn | 1547-6286 1555-8584 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj-art-a2b1d585a5ed49e18c68f69cffcd521e2025-01-30T15:18:13ZengTaylor & Francis GroupRNA Biology1547-62861555-85842025-02-0110.1080/15476286.2025.2459039Exploring RNA modifications in infectious non-coding circular RNAsPavel Vopalensky0Anton Škríba1Michela Chiumenti2Lucia Ďuričeková3Anna Šimonová4Ondřej Lukšan5Francesco di Serio6Beatriz Navarro7Hana Cahova8Institute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaInstitute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaInstitute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Bari, ItalyInstitute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaInstitute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaInstitute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaInstitute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Bari, ItalyInstitute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Bari, ItalyInstitute of Organic Chemistry and Biochemistry of the CAS, Prague, CzechiaViroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC – MS and Oxford Nanopore Technology (ONT) direct RNA sequencing. Although no modification was detected in ASBVd, CEVd contained approximately one m6A per RNA molecule. ONT sequencing predicted three m6A positions. Employing orthogonal SELECT method, we confirmed m6A in two positions A353 and A360, which are highly conserved among CEVd variants. These positions are located in the left terminal region of the CEVd rod-like structure where likely RNA Pol II and and TFIIIA-7ZF bind, thus suggesting potential biological role of methylation in viroid replication.https://www.tandfonline.com/doi/10.1080/15476286.2025.2459039ViroidRNA modification6-methyladenosinedirect rna-seqLC-MS, m6A SELECT |
| spellingShingle | Pavel Vopalensky Anton Škríba Michela Chiumenti Lucia Ďuričeková Anna Šimonová Ondřej Lukšan Francesco di Serio Beatriz Navarro Hana Cahova Exploring RNA modifications in infectious non-coding circular RNAs RNA Biology Viroid RNA modification 6-methyladenosine direct rna-seq LC-MS, m6A SELECT |
| title | Exploring RNA modifications in infectious non-coding circular RNAs |
| title_full | Exploring RNA modifications in infectious non-coding circular RNAs |
| title_fullStr | Exploring RNA modifications in infectious non-coding circular RNAs |
| title_full_unstemmed | Exploring RNA modifications in infectious non-coding circular RNAs |
| title_short | Exploring RNA modifications in infectious non-coding circular RNAs |
| title_sort | exploring rna modifications in infectious non coding circular rnas |
| topic | Viroid RNA modification 6-methyladenosine direct rna-seq LC-MS, m6A SELECT |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2025.2459039 |
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