Cargando…
NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes
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...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10101982/ https://www.ncbi.nlm.nih.gov/pubmed/37055518 http://dx.doi.org/10.1038/s42003-023-04774-6 |
_version_ | 1785025607093977088 |
---|---|
author | Sharma, Sunny Yang, Jun Favate, John Shah, Premal Kiledjian, Megerditch |
author_facet | Sharma, Sunny Yang, Jun Favate, John Shah, Premal Kiledjian, Megerditch |
author_sort | Sharma, Sunny |
collection | PubMed |
description | 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 m(7)G-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. |
format | Online Article Text |
id | pubmed-10101982 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-101019822023-04-15 NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes Sharma, Sunny Yang, Jun Favate, John Shah, Premal Kiledjian, Megerditch Commun Biol Article 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 m(7)G-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. Nature Publishing Group UK 2023-04-13 /pmc/articles/PMC10101982/ /pubmed/37055518 http://dx.doi.org/10.1038/s42003-023-04774-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Sharma, Sunny Yang, Jun Favate, John Shah, Premal Kiledjian, Megerditch NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes |
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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10101982/ https://www.ncbi.nlm.nih.gov/pubmed/37055518 http://dx.doi.org/10.1038/s42003-023-04774-6 |
work_keys_str_mv | AT sharmasunny nadcapproandcircncmethodsforaccurateprofilingofnadandnoncanonicalrnacapsineukaryotes AT yangjun nadcapproandcircncmethodsforaccurateprofilingofnadandnoncanonicalrnacapsineukaryotes AT favatejohn nadcapproandcircncmethodsforaccurateprofilingofnadandnoncanonicalrnacapsineukaryotes AT shahpremal nadcapproandcircncmethodsforaccurateprofilingofnadandnoncanonicalrnacapsineukaryotes AT kiledjianmegerditch nadcapproandcircncmethodsforaccurateprofilingofnadandnoncanonicalrnacapsineukaryotes |