دورية أكاديمية
Structured RNA Contaminants in Bacterial Ribo-Seq.
| العنوان: | Structured RNA Contaminants in Bacterial Ribo-Seq. |
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| المؤلفون: | Fremin BJ; Department of Genetics, Stanford University, Stanford, California, USA., Bhatt AS; Department of Genetics, Stanford University, Stanford, California, USA asbhatt@stanford.edu.; Department of Medicine (Hematology), Stanford University, Stanford, California, USA. |
| المصدر: | MSphere [mSphere] 2020 Oct 21; Vol. 5 (5). Date of Electronic Publication: 2020 Oct 21. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 101674533 Publication Model: Electronic Cited Medium: Internet ISSN: 2379-5042 (Electronic) Linking ISSN: 23795042 NLM ISO Abbreviation: mSphere Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, DC : American Society for Microbiology, [2015]- |
| مواضيع طبية MeSH: | Escherichia coli/*genetics , RNA, Untranslated/*chemistry , RNA, Untranslated/*genetics , Ribosomes/*genetics, Computational Biology ; Gene Expression Profiling ; Sequence Analysis, RNA |
| مستخلص: | Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes. For example, Escherichia coli Ribo-Seq libraries also capture reads from most noncoding RNAs (ncRNAs). While some of these ncRNAs may overlap coding regions, this alone does not explain the majority of observed signal across ncRNAs. These fragments of ncRNAs in Ribo-Seq data pass all size selection steps of the Ribo-Seq protocol and survive hours of micrococcal nuclease (MNase) treatment. In this work, we specifically focus on Ribo-Seq signal across ncRNAs and provide evidence to suggest that RNA structure, as opposed to ribosome binding, protects them from degradation and allows them to persist in the Ribo-Seq sequencing library preparation. By inspecting these "contaminant reads" in bacterial Ribo-Seq, we show that data previously disregarded in bacterial Ribo-Seq experiments may, in fact, be used to gain partial information regarding the in vivo secondary structure of ncRNAs. IMPORTANCE Structured ncRNAs are pivotal mediators of bioregulation in bacteria, and their functions are often reliant on their specific structures. Here, we first inspect Ribo-Seq reads across noncoding regions, identifying contaminant reads in these libraries. We observe that contaminant reads in bacterial Ribo-Seq experiments that are often disregarded, in fact, strongly overlap with structured regions of ncRNAs. We then perform several bioinformatic analyses to determine why these contaminant reads may persist in Ribo-Seq libraries. Finally, we highlight some structured RNA contaminants in Ribo-Seq and support the hypothesis that structures in the RNA protect them from MNase digestion. We conclude that researchers should be cautious when interpreting Ribo-Seq signal as coding without considering signal distribution. These findings also may enable us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large scale and in vivo through the reanalysis of existing Ribo-Seq data sets. (Copyright © 2020 Fremin and Bhatt.) |
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| معلومات مُعتمدة: | P50 AG047366 United States AG NIA NIH HHS; 1S10OD02014101 United States OD NIH HHS; DGE-114747 International National Science Foundation |
| فهرسة مساهمة: | Keywords: RNA structure; metagenomics; metatranscriptomics; microbiome |
| المشرفين على المادة: | 0 (RNA, Untranslated) |
| تواريخ الأحداث: | Date Created: 20201022 Date Completed: 20210720 Latest Revision: 20240403 |
| رمز التحديث: | 20240403 |
| مُعرف محوري في PubMed: | PMC7580957 |
| DOI: | 10.1128/mSphere.00855-20 |
| PMID: | 33087519 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2379-5042 |
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| DOI: | 10.1128/mSphere.00855-20 |