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Related Concept Videos

Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Related Experiment Video

Updated: Apr 12, 2026

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry
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Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics.

Rebecca E Rose1, Ryan Quinn1, Jackie L Sayre1

  • 1The RNA Institute, University at Albany, Albany, New York 12222, USA.

RNA (New York, N.Y.)
|May 22, 2015
PubMed
Summary

This study introduces a novel mass spectrometry method for comprehensively surveying RNA post-transcriptional modifications (PTMs) in cells. This technique enables global analysis of PTM levels, advancing our understanding of their biological significance.

Keywords:
RNAomicsepitranscriptomicsglobal profilingmass spectrometrymetabolomicsribonucleotide modifications

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Analytical Chemistry

Background:

  • Elucidating the biological roles of RNA post-transcriptional modifications (PTMs) is challenging due to a lack of high-throughput detection methods.
  • Existing sequencing approaches are insufficient for comprehensively tracking PTM levels under varying experimental conditions.

Purpose of the Study:

  • To develop a high-throughput strategy for global surveying of all ribonucleotide modifications within a cell.
  • To overcome limitations in current methods for detecting, locating, and quantifying RNA PTMs.

Main Methods:

  • Utilized direct infusion electrospray ionization mass spectrometry (ESI-MS) on whole cell extracts, bypassing chromatographic separation.
  • Employed accurate mass analysis for database-aided PTM identification.
  • Applied multistep tandem mass spectrometry (MS(n)) and consecutive reaction monitoring (CRM) for structural confirmation.
  • Leveraged ion mobility spectrometry mass spectrometry (IMS-MS) for generating unique modification profiles via heat-map plots.

Main Results:

  • Demonstrated a method for direct, global analysis of PTMs in complex ribonucleotide mixtures.
  • IMS-MS heat-maps provided distinct modification profiles for different cell types and metabolic states.
  • Established tRNA samples as reliable internal standards for quantitative PTM analysis.
  • Showcased the ability to compare PTM expression levels across different experimental conditions using intrinsic standards.

Conclusions:

  • The developed ESI-MS strategy offers a powerful tool for comprehensive RNA PTM profiling.
  • This approach facilitates the investigation of RNA modification system biology by enabling simultaneous evaluation of global PTM expression.
  • The findings provide new insights into the biological significance of RNA modifications and their regulatory networks.