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Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues.

Ni Pan1, Zhiwei Wang1, Bing Wang1

  • 1Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China.

Frontiers in Cell and Developmental Biology
|August 12, 2021
PubMed
Summary

Researchers identified over 1,000 microproteins, including novel ncRNA-encoded ones, in mouse tissues. These small proteins show tissue-specific functions, expanding our understanding of the mouse proteome.

Keywords:
de novo sequencingmouse tissuenon-coding RNAssmall open reading frametop-down

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Area of Science:

  • Proteomics
  • Molecular Biology
  • Genomics

Background:

  • Small open reading frame encoded peptides (SEPs), or microproteins, are crucial in biological processes.
  • Many microprotein open reading frames reside within non-coding RNA (ncRNA) regions.
  • ncRNA-encoded polypeptides have demonstrated essential functions across various tissues.

Purpose of the Study:

  • To comprehensively profile the proteomic characterization of microproteins in five mouse tissues.
  • To identify and characterize ncRNA-encoded microproteins, particularly those not present in current databases.
  • To investigate potential tissue-specific functions of microproteins.

Main Methods:

  • Utilized mass spectrometry with bottom-up, top-down, and de novo sequencing strategies.
  • Performed database-dependent searches against the OpenProt database.
  • Analyzed and annotated identified microproteins for functional domains and tissue distribution.

Main Results:

  • Identified a total of 1,074 microproteins, including 270 ncRNA-encoded microproteins.
  • Discovered 12 novel ncRNA-encoded microproteins not previously found in databases.
  • Observed tissue-specific enrichment of microproteins, with the brain showing the most neuropeptides and the spleen the most immunoassociated microproteins.
  • Predicted domains for unannotated microproteins, including macrophage migration inhibitory factor and Prefoldin domains.

Conclusions:

  • The study significantly expands the known mouse proteome by identifying numerous microproteins, especially those encoded by ncRNAs.
  • Microproteins exhibit tissue-specific functions, suggesting specialized roles in different organs.
  • The findings provide valuable insights into the molecular biology of mouse tissues and the functional significance of ncRNA-encoded proteins.