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RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosoma...

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Autores principales: Choe, Donghui, Szubin, Richard, Poudel, Saugat, Sastry, Anand, Song, Yoseb, Lee, Yongjae, Cho, Suhyung, Palsson, Bernhard, Cho, Byung-Kwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496792/
https://www.ncbi.nlm.nih.gov/pubmed/34570751
http://dx.doi.org/10.1371/journal.pgen.1009821
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author Choe, Donghui
Szubin, Richard
Poudel, Saugat
Sastry, Anand
Song, Yoseb
Lee, Yongjae
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
author_facet Choe, Donghui
Szubin, Richard
Poudel, Saugat
Sastry, Anand
Song, Yoseb
Lee, Yongjae
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
author_sort Choe, Donghui
collection PubMed
description RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.
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spelling pubmed-84967922021-10-08 RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics Choe, Donghui Szubin, Richard Poudel, Saugat Sastry, Anand Song, Yoseb Lee, Yongjae Cho, Suhyung Palsson, Bernhard Cho, Byung-Kwan PLoS Genet Research Article RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies. Public Library of Science 2021-09-27 /pmc/articles/PMC8496792/ /pubmed/34570751 http://dx.doi.org/10.1371/journal.pgen.1009821 Text en © 2021 Choe et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Choe, Donghui
Szubin, Richard
Poudel, Saugat
Sastry, Anand
Song, Yoseb
Lee, Yongjae
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title_full RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title_fullStr RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title_full_unstemmed RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title_short RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
title_sort riborid: a low cost, advanced, and ultra-efficient method to remove ribosomal rna for bacterial transcriptomics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496792/
https://www.ncbi.nlm.nih.gov/pubmed/34570751
http://dx.doi.org/10.1371/journal.pgen.1009821
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