Full-length direct RNA sequencing uncovers stress
granule-dependent RNA decay upon cellular stress

J 2024

Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

DAR, Showkat Ahmad; Sulochan MALLA; Vlastimil MARTINEK; Matthew John PAYEA; Christopher Tai-Yi LEE et al.

Základní údaje

Originální název

Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

Autoři

DAR, Showkat Ahmad; Sulochan MALLA; Vlastimil MARTINEK; Matthew John PAYEA; Christopher Tai-Yi LEE; Jessica MARTIN; Aditya Jignesh KHANDESHI; Jennifer L MARTINDALE; Cedric BELAIR a Manolis MARAGKAKIS

Vydání

eLife, ELIFE SCIENCES PUBLICATIONS LTD, 2024, 2050-084X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.400 v roce 2023

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/24:00138997

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.7554/eLife.96284

UT WoS

001394416900001

Klíčová slova anglicky

stress response; cell line; RNA decay

Štítky

143160, CF BIOIT, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 7. 2025 12:50, Mgr. Petra Trembecká, Ph.D.

Anotace

V originále

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 5' 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 5' 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.

Návaznosti

90267, velká výzkumná infrastruktura

Název: NCMG III

Citovat

DAR, Showkat Ahmad; Sulochan MALLA; Vlastimil MARTINEK; Matthew John PAYEA; Christopher Tai-Yi LEE; Jessica MARTIN; Aditya Jignesh KHANDESHI; Jennifer L MARTINDALE; Cedric BELAIR a Manolis MARAGKAKIS. Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress. eLife. ELIFE SCIENCES PUBLICATIONS LTD, 2024, roč. 13, December, s. 1-22. ISSN 2050-084X. Dostupné z: https://doi.org/10.7554/eLife.96284.

@article{2481877,
   author = {Dar, Showkat Ahmad and Malla, Sulochan and Martinek, Vlastimil and Payea, Matthew John and Lee, Christopher TaiandYi and Martin, Jessica and Khandeshi, Aditya Jignesh and Martindale, Jennifer L and Belair, Cedric and Maragkakis, Manolis},
   article_number = {December},
   doi = {https://doi.org/10.7554/eLife.96284},
   keywords = {stress response; cell line; RNA decay},
   language = {eng},
   issn = {2050-084X},
   journal = {eLife},
   title = {Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress},
   url = {https://elifesciences.org/articles/96284},
   volume = {13},
   year = {2024}
}

TY  - JOUR
ID  - 2481877
AU  - Dar, Showkat Ahmad - Malla, Sulochan - Martinek, Vlastimil - Payea, Matthew John - Lee, Christopher Tai-Yi - Martin, Jessica - Khandeshi, Aditya Jignesh - Martindale, Jennifer L - Belair, Cedric - Maragkakis, Manolis
PY  - 2024
TI  - Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress
JF  - eLife
VL  - 13
IS  - December
SP  - 1-22
EP  - 1-22
PB  - ELIFE SCIENCES PUBLICATIONS LTD
SN  - 2050084X
KW  - stress response
KW  - cell line
KW  - RNA decay
UR  - https://elifesciences.org/articles/96284
N2  - 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 5' 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 5' 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.
ER  -

DAR, Showkat Ahmad; Sulochan MALLA; Vlastimil MARTINEK; Matthew John PAYEA; Christopher Tai-Yi LEE; Jessica MARTIN; Aditya Jignesh KHANDESHI; Jennifer L MARTINDALE; Cedric BELAIR a Manolis MARAGKAKIS. Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress. \textit{eLife}. ELIFE SCIENCES PUBLICATIONS LTD, 2024, roč.~13, December, s.~1-22. ISSN~2050-084X. Dostupné z: https://doi.org/10.7554/eLife.96284.

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