Molecular Cell
Volume 80, Issue 5, 3 December 2020, Pages 892-902.e4
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Functional Atlas of Primary miRNA Maturation by the Microprocessor

https://doi.org/10.1016/j.molcel.2020.10.028Get rights and content
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Highlights

  • Microprocessor activity across miRBase is profiled in vitro using Dro-seq

  • High-throughput mutagenesis allows analysis at single-nucleotide resolution

  • A functional atlas of primary miRNA maturation by the Microprocessor is described

  • Pri-miRNAs with low Shannon entropy are superior substrates for Drosha

Summary

Primary microRNAs (miRNAs) are the precursors of miRNAs that modulate the expression of most mRNAs in humans. They fold up into a hairpin structure that is cleaved at its base by an enzyme complex known as the Microprocessor (Drosha/DGCR8). While many of the molecular details are known, a complete understanding of what features distinguish primary miRNA from hairpin structures in other transcripts is still lacking. We develop a massively parallel functional assay termed Dro-seq (Drosha sequencing) that enables testing of hundreds of known primary miRNA substrates and thousands of single-nucleotide variants. We find an additional feature of primary miRNAs, called Shannon entropy, describing the structural ensemble important for processing. In a deep mutagenesis experiment, we observe particular apical loop U bases, likely recognized by DGCR8, are important for efficient processing. These findings build on existing knowledge about primary miRNA maturation by the Microprocessor and further explore the substrate RNA sequence-structure relationship.

Keywords

microprocessor
miRNA biogenesis
DROSHA
RNA structure
Dro-seq
pri-miRNA
Shannon entropy

Cited by (0)

2

Present address: Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA 02210, USA

3

Present address: Montai Health, Inc., 75 Moulton Street, Cambridge, MA 02138, USA

4

Lead Contact