Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research..
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3' status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:50 |
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| Enthalten in: |
Nucleic acids research - 50(2022), 9 vom: 20. Mai, Seite 5029-5046 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Herzel, Lydia [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 24.05.2022 Date Revised 16.07.2022 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/nar/gkac295 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM340530626 |
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| 520 | |a © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. | ||
| 520 | |a Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3' status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs | ||
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| 700 | 1 | |a Yao, Chun-Chen |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Gene-Wei |e verfasserin |4 aut | |
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