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Related Concept Videos

RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

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Related Experiment Video

Updated: May 13, 2026

Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing
06:57

Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing

Published on: July 7, 2023

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.

Maxime Wery1, Marc Descrimes, Claude Thermes

  • 1ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.

Methods (San Diego, Calif.)
|March 26, 2013
PubMed
Summary

Choosing the right RNA fragmentation method is crucial for accurate RNA sequencing (RNA-Seq) analysis. Zinc-mediated fragmentation offers more robust transcriptome reassembly and transcript identification compared to RNase III.

Keywords:
RNA-SeqRNase IIISegmentationZinc fragmentationncRNA

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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing
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Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing

Published on: July 7, 2023

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Whole transcriptome RNA sequencing (RNA-Seq) is vital for gene expression analysis and novel RNA discovery.
  • RNA fragmentation is a key library preparation step, with various commercial methods available.
  • The impact of different RNA fragmentation techniques on transcriptome analysis remains largely uncharacterized.

Purpose of the Study:

  • To compare the effects of RNase III and zinc-mediated RNA fragmentation on transcript expression measurement.
  • To evaluate the influence of these fragmentation methods on transcriptome reassembly.
  • To determine the optimal RNA fragmentation technique for accurate transcript identification.

Main Methods:

  • Comparison of RNase III- and zinc-mediated RNA fragmentation protocols.
  • Analysis of RNA-Seq data for transcript expression measurement.
  • Assessment of transcriptome reassembly accuracy and transcript end-point precision.

Main Results:

  • RNase III fragmentation exhibits heterogeneity along transcripts, impacting autocorrelation.
  • Abundant non-coding RNAs are underrepresented using RNase III fragmentation.
  • Zinc-mediated fragmentation improves transcriptome reassembly and 5'/3' end precision.

Conclusions:

  • Transcriptome reassembly from RNA-Seq data is highly sensitive to the RNA fragmentation method used.
  • Zinc-mediated fragmentation yields more accurate and robust transcript identification than RNase III.
  • The choice of fragmentation technique significantly influences the reliability of RNA-Seq-based transcriptomic studies.