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Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
BACKGROUND: Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyoge...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751559/ https://www.ncbi.nlm.nih.gov/pubmed/29297355 http://dx.doi.org/10.1186/s12859-017-1897-0 |
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author | Rath, Ethan C. Pitman, Stephanie Cho, Kyu Hong Bai, Yongsheng |
author_facet | Rath, Ethan C. Pitman, Stephanie Cho, Kyu Hong Bai, Yongsheng |
author_sort | Rath, Ethan C. |
collection | PubMed |
description | BACKGROUND: Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III. The endoribonuclease RNase III cleaves double stranded RNAs, which can be formed during the interaction between an sRNA and target mRNAs. RESULTS: For this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type. First, we developed a custom script that can detect intergenic regions of the S. pyogenes genome. A differential expression analysis with Cufflinks and Stringtie was then performed to identify the intergenic regions whose expression was influenced by the RNase III gene deletion. CONCLUSION: This analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs. This study not only expanded our knowledge on novel sRNAs but would also give us new insight into sRNA degradation. |
format | Online Article Text |
id | pubmed-5751559 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57515592018-01-05 Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data Rath, Ethan C. Pitman, Stephanie Cho, Kyu Hong Bai, Yongsheng BMC Bioinformatics Research BACKGROUND: Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III. The endoribonuclease RNase III cleaves double stranded RNAs, which can be formed during the interaction between an sRNA and target mRNAs. RESULTS: For this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type. First, we developed a custom script that can detect intergenic regions of the S. pyogenes genome. A differential expression analysis with Cufflinks and Stringtie was then performed to identify the intergenic regions whose expression was influenced by the RNase III gene deletion. CONCLUSION: This analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs. This study not only expanded our knowledge on novel sRNAs but would also give us new insight into sRNA degradation. BioMed Central 2017-12-28 /pmc/articles/PMC5751559/ /pubmed/29297355 http://dx.doi.org/10.1186/s12859-017-1897-0 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Rath, Ethan C. Pitman, Stephanie Cho, Kyu Hong Bai, Yongsheng Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title | Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title_full | Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title_fullStr | Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title_full_unstemmed | Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title_short | Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data |
title_sort | identification of streptococcal small rnas that are putative targets of rnase iii through bioinformatics analysis of rna sequencing data |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751559/ https://www.ncbi.nlm.nih.gov/pubmed/29297355 http://dx.doi.org/10.1186/s12859-017-1897-0 |
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