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Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5’ and 3’ termini of the same transcript remain scarce....

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Detalles Bibliográficos
Autores principales: Ju, Xiangwu, Li, Dayi, Liu, Shixin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814526/
https://www.ncbi.nlm.nih.gov/pubmed/31308523
http://dx.doi.org/10.1038/s41564-019-0500-z
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author Ju, Xiangwu
Li, Dayi
Liu, Shixin
author_facet Ju, Xiangwu
Li, Dayi
Liu, Shixin
author_sort Ju, Xiangwu
collection PubMed
description The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5’ and 3’ termini of the same transcript remain scarce. Here we present SEnd-seq—a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution. Using this method, we obtain a comprehensive view of the Escherichia coli transcriptome, which displays an unexpected level of complexity. SEnd-seq significantly expands the catalog of transcription start sites and termination sites, defines unique transcription units, and detects prevalent antisense RNA. Strikingly, our results unveil widespread overlapping bidirectional terminators located between opposing gene pairs. We further show that convergent transcription is a major contributor to highly efficient bidirectional termination both in vitro and in vivo. This finding highlights an underappreciated role of RNA polymerase conflicts in shaping transcript boundaries and suggests an evolutionary strategy for modulating transcriptional output by arranging gene orientation.
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spelling pubmed-68145262020-01-15 Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria Ju, Xiangwu Li, Dayi Liu, Shixin Nat Microbiol Article The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5’ and 3’ termini of the same transcript remain scarce. Here we present SEnd-seq—a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution. Using this method, we obtain a comprehensive view of the Escherichia coli transcriptome, which displays an unexpected level of complexity. SEnd-seq significantly expands the catalog of transcription start sites and termination sites, defines unique transcription units, and detects prevalent antisense RNA. Strikingly, our results unveil widespread overlapping bidirectional terminators located between opposing gene pairs. We further show that convergent transcription is a major contributor to highly efficient bidirectional termination both in vitro and in vivo. This finding highlights an underappreciated role of RNA polymerase conflicts in shaping transcript boundaries and suggests an evolutionary strategy for modulating transcriptional output by arranging gene orientation. 2019-07-15 2019-11 /pmc/articles/PMC6814526/ /pubmed/31308523 http://dx.doi.org/10.1038/s41564-019-0500-z Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Ju, Xiangwu
Li, Dayi
Liu, Shixin
Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title_full Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title_fullStr Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title_full_unstemmed Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title_short Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria
title_sort full-length rna profiling reveals pervasive bidirectional transcription terminators in bacteria
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814526/
https://www.ncbi.nlm.nih.gov/pubmed/31308523
http://dx.doi.org/10.1038/s41564-019-0500-z
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