Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.

Ribosomes / metabolism RNA, Messenger / metabolism Protein Biosynthesis Humans Transcriptome RNA, Ribosomal / metabolism High-Throughput Nucleotide Sequencing Calibration Heat-Shock Response / genetics Ribosome Profiling

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
26 Aug 2024
Historique:
received: 09 07 2023
accepted: 02 08 2024
medline: 27 8 2024
pubmed: 27 8 2024
entrez: 26 8 2024
Statut: epublish

Résumé

Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.

Identifiants

DOI: 10.1038/s41467-024-51258-0 PMID: 39187487
pubmed: 39187487
doi: 10.1038/s41467-024-51258-0
pii: 10.1038/s41467-024-51258-0
doi:

Substances chimiques

RNA, Messenger 0
RNA, Ribosomal 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

7061

Subventions

Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP20H05784
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP24H02307
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP20H05782
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP24H02306
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP20H05786
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP24H02307
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP21H05734
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP23H04268
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP20gm1410001
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP20gm1410001
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23gm6910005
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP22fk0108570
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23H02415
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23H00095
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP21K15023
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23K05648
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP22K20765
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23K14173
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23KJ2178
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23KJ2175
Organisme : MEXT | RIKEN
ID : Pioneering Project
Organisme : MEXT | RIKEN
ID : RIKEN TRIP initiative "TRIP-AGIS"
Organisme : MEXT | RIKEN
ID : Pioneering Project
Organisme : MEXT | Japan Science and Technology Agency (JST)
ID : JPMJBS2418
Organisme : MEXT | Japan Science and Technology Agency (JST)
ID : JPMJFR226F

Informations de copyright

© 2024. The Author(s).

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Auteurs

Kotaro Tomuro (K)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
ORCID: 0009-0008-3513-4507

Mari Mito (M)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.

Hirotaka Toh (H)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
ORCID: 0000-0003-0753-0787

Naohiro Kawamoto (N)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
ORCID: 0000-0003-4252-0963

Takahito Miyake (T)

Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
ORCID: 0000-0002-4356-5883

Siu Yu A Chow (SYA)

Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan.

Masao Doi (M)

Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
ORCID: 0000-0001-6264-9217

Yoshiho Ikeuchi (Y)

Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan.
Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
ORCID: 0000-0002-2829-3840

Yuichi Shichino (Y)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan. yuichi.shichino@riken.jp.
ORCID: 0000-0002-0093-1185

Shintaro Iwasaki (S)

RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan. shintaro.iwasaki@riken.jp.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan. shintaro.iwasaki@riken.jp.
ORCID: 0000-0001-7724-3754

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Classifications MeSH

questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Ribosomes › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Biosynthèse des protéines › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Techniques d'investigation › Poids et mesures › Calibrage › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Phénomènes physiologiques › Stress physiologique › Réaction de choc thermique › Calibrated ribosome profiling assesses the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Profilage de ribosome › Calibrated ribosome profiling assesses the...