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SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle
RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling a...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10568207/ http://dx.doi.org/10.15252/msb.202211427 |
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author | Liu, Haiyue Arsiè, Roberto Schwabe, Daniel Schilling, Marcel Minia, Igor Alles, Jonathan Boltengagen, Anastasiya Kocks, Christine Falcke, Martin Friedman, Nir Landthaler, Markus Rajewsky, Nikolaus |
author_facet | Liu, Haiyue Arsiè, Roberto Schwabe, Daniel Schilling, Marcel Minia, Igor Alles, Jonathan Boltengagen, Anastasiya Kocks, Christine Falcke, Martin Friedman, Nir Landthaler, Markus Rajewsky, Nikolaus |
author_sort | Liu, Haiyue |
collection | PubMed |
description | RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes. |
format | Online Article Text |
id | pubmed-10568207 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-105682072023-10-13 SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle Liu, Haiyue Arsiè, Roberto Schwabe, Daniel Schilling, Marcel Minia, Igor Alles, Jonathan Boltengagen, Anastasiya Kocks, Christine Falcke, Martin Friedman, Nir Landthaler, Markus Rajewsky, Nikolaus Mol Syst Biol Method RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes. John Wiley and Sons Inc. 2023-08-28 /pmc/articles/PMC10568207/ http://dx.doi.org/10.15252/msb.202211427 Text en © 2023 The Authors. Published under the terms of the CC BY 4.0 license https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Method Liu, Haiyue Arsiè, Roberto Schwabe, Daniel Schilling, Marcel Minia, Igor Alles, Jonathan Boltengagen, Anastasiya Kocks, Christine Falcke, Martin Friedman, Nir Landthaler, Markus Rajewsky, Nikolaus SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title |
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title_full |
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title_fullStr |
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title_full_unstemmed |
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title_short |
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle |
title_sort | slam‐drop‐seq reveals mrna kinetic rates throughout the cell cycle |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10568207/ http://dx.doi.org/10.15252/msb.202211427 |
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