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 rib...

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Autores principales:	Donghui Choe, Richard Szubin, Saugat Poudel, Anand Sastry, Yoseb Song, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/0b37f4265fd34603afb9aa90ebbc369b
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spelling	oai:doaj.org-article:0b37f4265fd34603afb9aa90ebbc369b2021-12-02T20:03:18ZRiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.1553-73901553-740410.1371/journal.pgen.1009821https://doaj.org/article/0b37f4265fd34603afb9aa90ebbc369b2021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009821https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404RNA 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.Donghui ChoeRichard SzubinSaugat PoudelAnand SastryYoseb SongYongjae LeeSuhyung ChoBernhard PalssonByung-Kwan ChoPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 9, p e1009821 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Donghui Choe Richard Szubin Saugat Poudel Anand Sastry Yoseb Song Yongjae Lee Suhyung Cho Bernhard Palsson Byung-Kwan Cho RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.
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.
format	article
author	Donghui Choe Richard Szubin Saugat Poudel Anand Sastry Yoseb Song Yongjae Lee Suhyung Cho Bernhard Palsson Byung-Kwan Cho
author_facet	Donghui Choe Richard Szubin Saugat Poudel Anand Sastry Yoseb Song Yongjae Lee Suhyung Cho Bernhard Palsson Byung-Kwan Cho
author_sort	Donghui Choe
title	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_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_sort	riborid: a low cost, advanced, and ultra-efficient method to remove ribosomal rna for bacterial transcriptomics.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/0b37f4265fd34603afb9aa90ebbc369b
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RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.

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