NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes
Abstract Accurate identification of NAD-capped RNAs is essential for delineating their generation and biological function. Previous transcriptome-wide methods used to classify NAD-capped RNAs in eukaryotes contain inherent limitations that have hindered the accurate identification of NAD caps from e...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-04774-6 |
| _version_ | 1797845844822589440 |
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| author | Sunny Sharma Jun Yang John Favate Premal Shah Megerditch Kiledjian |
| author_facet | Sunny Sharma Jun Yang John Favate Premal Shah Megerditch Kiledjian |
| author_sort | Sunny Sharma |
| collection | DOAJ |
| description | Abstract Accurate identification of NAD-capped RNAs is essential for delineating their generation and biological function. Previous transcriptome-wide methods used to classify NAD-capped RNAs in eukaryotes contain inherent limitations that have hindered the accurate identification of NAD caps from eukaryotic RNAs. In this study, we introduce two orthogonal methods to identify NAD-capped RNAs more precisely. The first, NADcapPro, uses copper-free click chemistry and the second is an intramolecular ligation-based RNA circularization, circNC. Together, these methods resolve the limitations of previous methods and allowed us to discover unforeseen features of NAD-capped RNAs in budding yeast. Contrary to previous reports, we find that 1) cellular NAD-RNAs can be full-length and polyadenylated transcripts, 2) transcription start sites for NAD-capped and canonical m7G-capped RNAs can be different, and 3) NAD caps can be added subsequent to transcription initiation. Moreover, we uncovered a dichotomy of NAD-RNAs in translation where they are detected with mitochondrial ribosomes but minimally on cytoplasmic ribosomes indicating their propensity to be translated in mitochondria. |
| first_indexed | 2024-04-09T17:45:31Z |
| format | Article |
| id | doaj.art-edbfc8cb2da542768d8bc857e4189f85 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-04-09T17:45:31Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-edbfc8cb2da542768d8bc857e4189f852023-04-16T11:22:43ZengNature PortfolioCommunications Biology2399-36422023-04-016111410.1038/s42003-023-04774-6NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotesSunny Sharma0Jun Yang1John Favate2Premal Shah3Megerditch Kiledjian4Department of Cell Biology and Neurosciences, Rutgers UniversityDepartment of Cell Biology and Neurosciences, Rutgers UniversityDepartment of Genetics, Rutgers UniversityDepartment of Genetics, Rutgers UniversityDepartment of Cell Biology and Neurosciences, Rutgers UniversityAbstract Accurate identification of NAD-capped RNAs is essential for delineating their generation and biological function. Previous transcriptome-wide methods used to classify NAD-capped RNAs in eukaryotes contain inherent limitations that have hindered the accurate identification of NAD caps from eukaryotic RNAs. In this study, we introduce two orthogonal methods to identify NAD-capped RNAs more precisely. The first, NADcapPro, uses copper-free click chemistry and the second is an intramolecular ligation-based RNA circularization, circNC. Together, these methods resolve the limitations of previous methods and allowed us to discover unforeseen features of NAD-capped RNAs in budding yeast. Contrary to previous reports, we find that 1) cellular NAD-RNAs can be full-length and polyadenylated transcripts, 2) transcription start sites for NAD-capped and canonical m7G-capped RNAs can be different, and 3) NAD caps can be added subsequent to transcription initiation. Moreover, we uncovered a dichotomy of NAD-RNAs in translation where they are detected with mitochondrial ribosomes but minimally on cytoplasmic ribosomes indicating their propensity to be translated in mitochondria.https://doi.org/10.1038/s42003-023-04774-6 |
| spellingShingle | Sunny Sharma Jun Yang John Favate Premal Shah Megerditch Kiledjian NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes Communications Biology |
| title | NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
| title_full | NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
| title_fullStr | NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
| title_full_unstemmed | NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
| title_short | NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
| title_sort | nadcappro and circnc methods for accurate profiling of nad and non canonical rna caps in eukaryotes |
| url | https://doi.org/10.1038/s42003-023-04774-6 |
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