Global identification of functional microRNA-mRNA interactions in Drosophila

Hans-Hermann Wessels, Svetlana Lebedeva, Antje Hirsekorn, Ricardo Wurmus, Altuna Akalin, Neelanjan Mukherjee and Uwe Ohler ()
Additional contact information
Hans-Hermann Wessels: Max-Delbrück-Center for Molecular Medicine
Svetlana Lebedeva: Max-Delbrück-Center for Molecular Medicine
Antje Hirsekorn: Max-Delbrück-Center for Molecular Medicine
Ricardo Wurmus: Max-Delbrück-Center for Molecular Medicine
Altuna Akalin: Max-Delbrück-Center for Molecular Medicine
Neelanjan Mukherjee: Max-Delbrück-Center for Molecular Medicine
Uwe Ohler: Max-Delbrück-Center for Molecular Medicine

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: 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.

Date: 2019
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-019-09586-z Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09586-z

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-019-09586-z

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().