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Updated: Jun 8, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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A functional connection between the Microprocessor and a variant NEXT complex.

Katsutoshi Imamura1, William Garland2, Manfred Schmid2

  • 1Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark; Department of Systems Medicine, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.

Molecular Cell
|November 8, 2024
PubMed
Summary
This summary is machine-generated.

The Microprocessor complex processes primary miRNAs, and its DGCR8 protein links to the NEXT complex. This partnership targets specific RNA structures in mouse embryonic stem cells, revealing a new RNA degradation pathway.

Keywords:
DGCR8MicroprocessorNEXT complexRNA structureZCCHC8nuclear RNA decay

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Regulation

Background:

  • Primary microRNAs (miRNAs) are processed by the Microprocessor complex (DROSHA-DGCR8) in mammalian cells.
  • The RNA exosome pathway degrades various RNA substrates, but its specific targeting mechanisms are still being elucidated.

Purpose of the Study:

  • To investigate the fate of 5' flanking regions generated after Microprocessor cleavage of primary miRNAs.
  • To identify the protein complexes involved in the turnover of these RNA fragments and other structured RNAs.

Main Methods:

  • Biochemical assays to study protein-RNA interactions.
  • Mutagenesis studies to probe the function of specific protein domains.
  • Analysis of RNA processing and degradation in mouse embryonic stem cells (mESCs).

Main Results:

  • The nuclear exosome targeting (NEXT) complex, specifically its ZCCHC8 component, physically interacts with DGCR8.
  • A variant NEXT complex, comprising MTR4 and ZCCHC8 but lacking RBM7, is responsible for targeting stem-loop containing RNAs, including those derived from Microprocessor activity.
  • This MTR4-ZCCHC8 complex also targets other structured RNAs, such as those from enhancers, demonstrating substrate flexibility.

Conclusions:

  • The MTR4-ZCCHC8 NEXT complex links with Microprocessor (DGCR8/DROSHA) to degrade specific RNA structures.
  • RNA structural context dictates targeting by either the RBM7-containing or DGCR8-linked NEXT complex, revealing a sophisticated RNA surveillance mechanism.