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Transcriptome-Wide Profiling of RNA Stability.

Nina Fasching1, Jan Petržílek1,2, Niko Popitsch1

  • 1IMBA-Institute of Molecular Biotechnology, Vienna Biocenter (VBC), Vienna, Austria.

Methods in Molecular Biology (Clifton, N.J.)
|October 25, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces SLAMseq, a novel method for precisely measuring RNA stability and turnover rates in cells. This technique enhances our understanding of gene expression dynamics by providing accurate transcript half-lives.

Keywords:
4-ThiouridineGene regulationMetabolic RNA sequencingRNA stabilitySLAMseq

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Gene expression regulation involves RNA transcription and turnover.
  • Quantifying RNA biogenesis and decay contributions to steady-state transcript levels is challenging.
  • Conventional transcriptomics lacks the temporal resolution for kinetic parameter derivation.

Purpose of the Study:

  • To develop a protocol for genomic-scale RNA stability determination.
  • To provide accurate transcript half-lives using time-resolved transcriptomics.
  • To enable direct measurement of cellular RNA turnover kinetics.

Main Methods:

  • Metabolic RNA labeling with 4-thiouridine.
  • Chemical nucleoside conversion and whole-transcriptome sequencing.
  • SLAMseq (thiol-linked alkylation for metabolic sequencing of RNA) for time-resolved transcriptomics.

Main Results:

  • SLAMseq provides accurate transcript half-lives across the genome.
  • The method includes by-products of transcription, such as introns.
  • Enables genomic-scale determination of RNA stability.

Conclusions:

  • SLAMseq enhances traditional RNA sequencing protocols.
  • Acquires temporal resolution for direct measurement of RNA turnover.
  • Facilitates understanding of gene expression regulation under physiological conditions.