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

PloS One
Emily K FowlerTracey Chapman

Abstract

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 targe...Continue Reading

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Citations

Feb 6, 2019·Non-coding RNA·Marine LambertPatrick Provost
Mar 19, 2020·RNA Biology·Domenico RosaceSandra Blanco
Jun 12, 2020·Frontiers in Bioengineering and Biotechnology·Valentina PalmieriMassimiliano Papi
Dec 8, 2021·Evolution; International Journal of Organic Evolution·Cosima HotzySimone Immler

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Datasets Mentioned

BETA
GSE86313
GSE98833
GSE99673

Methods Mentioned

BETA
sRNA-seq
electrophoresis
PCR
RNA-seq

Software Mentioned

FastQC
PatMaN
R scripts
Perl
BaseClear
UEA sRNA Workbench

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