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Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis.

Dongliang Yu1, Min Xu1, Hidetaka Ito2

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|November 30, 2018
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Degradome sequencing (degradome-seq) effectively tracks microRNA (miRNA) precursor processing. This method supports miRNA annotation and reveals novel processing models.

Keywords:
degradomemicroRNA annotationsingle-stranded croppingtissue-/cell line-specific“loop-to-base” processing

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • MicroRNA (miRNA) target identification commonly uses degradome sequencing (degradome-seq).
  • The utility of degradome-seq for analyzing miRNA processing intermediates remains underexplored.

Purpose of the Study:

  • To investigate the application of degradome-seq data in tracking miRNA processing intermediates.
  • To evaluate the reliability of degradome-seq for miRNA annotation and processing pathway elucidation.

Main Methods:

  • Degradome-seq data analysis using a signal-to-noise ratio to identify prominent signals on miRNA precursors across 15 species.
  • Comparison of processing signal support for high-confidence versus low-confidence miRNAs in miRBase.
  • Assessment of degradome sampling diversity's impact on processing signal detection.

Main Results:

  • Degradome-seq data provided evidence for the processing of numerous miRNA precursors across analyzed species.
  • High-confidence miRNAs showed significantly higher support from degradome-seq data compared to low-confidence ones.
  • Increased degradome sampling diversity correlated with a higher percentage of miRNAs exhibiting processing signals.
  • Tissue- or cell line-specific processing patterns of miRNA precursors influenced mature miRNA accumulation.
  • A novel model of miRNA precursor processing, termed "single-stranded cropping," was proposed, with "loop-to-base" processing being more common than previously assumed.

Conclusions:

  • Degradome-seq is a powerful tool for tracking miRNA processing signals and enhancing miRNA annotation.
  • The study reveals insights into miRNA precursor processing mechanisms and their tissue-specific regulation.
  • Findings support the refinement of miRNA databases and underscore the importance of degradome-seq in miRNA research.