Global identification of functional microRNA-mRNA interactions in Drosophila

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Item Type:

Article

Title:

Global identification of functional microRNA-mRNA interactions in Drosophila

Creators Name:

Wessels, H.H. and Lebedeva, S. and Hirsekorn, A. and Wurmus, R. and Akalin, A. and Mukherjee, N. and Ohler, U.

Abstract:

MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.

Keywords:

Argonaute Proteins, Drosophila Proteins, Gene Expression Regulation, Messenger RNA, MicroRNAs, RNA Sequence Analysis, Transcriptome, Animals, Drosophila melanogaster

Source:

Nature Communications

ISSN:

2041-1723

Publisher:

Nature Publishing Group

Volume:

Number:

Page Range:

1626

Date:

9 April 2019