دورية أكاديمية
أعرض في EDS

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues.

التفاصيل البيبلوغرافية
العنوان: Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues.
المؤلفون: Fowler EK; School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom., Mohorianu I; School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom.; School of Computing Sciences, University of East Anglia, Norwich Research Park, United Kingdom., Smith DT; School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom., Dalmay T; School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom., Chapman T; School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom.
المصدر: PloS one [PLoS One] 2018 Feb 23; Vol. 13 (2), pp. e0191966. Date of Electronic Publication: 2018 Feb 23 (Print Publication: 2018).
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Drosophila melanogaster/*physiology , RNA/*metabolism, Animals ; RNA Interference ; Reproduction
مستخلص: RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5' and 3' terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified "rRNA blocking" protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues.
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معلومات مُعتمدة: BB/H008047/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/L003139/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20180224 Date Completed: 20180319 Latest Revision: 20220403
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC5825024
DOI: 10.1371/journal.pone.0191966
PMID: 29474379
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0191966