Global identification of functional microRNA::mRNA interactions in Drosophila

Item Type:

Preprint

Title:

Creators Name:

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

Abstract:

MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. Although Drosophila has been of critical importance for miRNA discovery, biogenesis and function, there has been no comprehensive experimental annotation of functional miRNA target sites. T close this gap, we generated the first in vivo map of miRNA::mRNA interactions in Drosophila melanogaster, making use of crosslinked nucleotides in Argonaute (AGO) crosslinking and immunoprecipitation (CLIP) experiments that enable an unambiguous assignment of miRNAs to AGO binding sites at much higher signal-to-noise ratio than computational predictions alone. Absolute quantification of cellular miRNA levels showed the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two different CLIP approaches, we identified a similar predictive potential to unambiguously assign thousands of miRNA::mRNA pairs from AGO1 interaction data at unprecedented depth. Quantitative RNA-Seq and subcodon-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 as well as their quantitative functional impact in Drosophila.

Keywords:

AGO1, microRNA, HITSCLIP, PARCLIP, RNA-Binding Proteins, Posttranscriptional Gene Expression Regulation, Animals, Drosophila

Source:

bioRxiv

Title of Book:

Global identification of functional microRNA::mRNA interactions in Drosophila

Publisher:

Cold Spring Harbor Laboratory Press

Article Number:

395335

Date:

22 August 2018

Official Publication:

https://doi.org/10.1101/395335

Related to:

URL	URL Type
https://edoc.mdc-berlin.de/18112/	Final version

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