Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress
Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear....
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2024-12-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/96284 |
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| author | Showkat Ahmad Dar Sulochan Malla Vlastimil Martinek Matthew John Payea Christopher Tai-Yi Lee Jessica Martin Aditya Jignesh Khandeshi Jennifer L Martindale Cedric Belair Manolis Maragkakis |
| author_facet | Showkat Ahmad Dar Sulochan Malla Vlastimil Martinek Matthew John Payea Christopher Tai-Yi Lee Jessica Martin Aditya Jignesh Khandeshi Jennifer L Martindale Cedric Belair Manolis Maragkakis |
| author_sort | Showkat Ahmad Dar |
| collection | DOAJ |
| description | Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5ʹ end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5ʹ end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation. |
| format | Article |
| id | doaj-art-34e5ddc7174d41d08480a88894c08ed0 |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-34e5ddc7174d41d08480a88894c08ed02025-08-20T01:58:33ZengeLife Sciences Publications LtdeLife2050-084X2024-12-011310.7554/eLife.96284Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stressShowkat Ahmad Dar0https://orcid.org/0000-0002-5077-1925Sulochan Malla1https://orcid.org/0000-0001-9957-4597Vlastimil Martinek2https://orcid.org/0000-0002-3204-1830Matthew John Payea3https://orcid.org/0000-0002-1960-4563Christopher Tai-Yi Lee4https://orcid.org/0000-0002-8621-256XJessica Martin5https://orcid.org/0009-0000-0830-9289Aditya Jignesh Khandeshi6https://orcid.org/0009-0004-8541-1702Jennifer L Martindale7https://orcid.org/0000-0002-3234-6861Cedric Belair8https://orcid.org/0000-0003-4007-2060Manolis Maragkakis9https://orcid.org/0000-0002-3158-1763Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United States; Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech RepublicLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesLaboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, United StatesCells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5ʹ end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5ʹ end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation.https://elifesciences.org/articles/96284stress responsecell lineRNA decay |
| spellingShingle | Showkat Ahmad Dar Sulochan Malla Vlastimil Martinek Matthew John Payea Christopher Tai-Yi Lee Jessica Martin Aditya Jignesh Khandeshi Jennifer L Martindale Cedric Belair Manolis Maragkakis Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress eLife stress response cell line RNA decay |
| title | Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress |
| title_full | Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress |
| title_fullStr | Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress |
| title_full_unstemmed | Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress |
| title_short | Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress |
| title_sort | full length direct rna sequencing uncovers stress granule dependent rna decay upon cellular stress |
| topic | stress response cell line RNA decay |
| url | https://elifesciences.org/articles/96284 |
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