Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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...
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...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.

Nucleic acids research·2026
Same author

Vaspin identified as a DNA-binding serpin with functional consequences for protease inhibition.

The FEBS journal·2025
Same author

Armless hairpin-like tRNAs in Romanomermis culicivorax: Evolutionary adaptation of a mitochondrial elongation factor EF-Tu.

The Journal of biological chemistry·2025
Same author

Targeting Glioblastoma Stem Cells via EphA2: Structural Insights into the RNA Aptamer A40s for Precision Therapy.

Journal of chemical information and modeling·2025
Same author

An alternative adaptation strategy of the CCA-adding enzyme to accept noncanonical tRNA substrates in Ascaris suum.

The Journal of biological chemistry·2025
Same author

Two complementing <i>in vivo</i> selection systems based on CCA-trimming exonucleases as a tool to monitor, select and evaluate enzymatic features of tRNA nucleotidyltransferases.

RNA biology·2025

Related Experiment Video

Updated: May 11, 2026

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

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

Gero Doose1, Maria Alexis, Rebecca Kirsch

  • 1Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Leipzig, Germany; Transcriptome Bioinformatics; LIFE - Leipzig Research Center for Civilization Diseases; University of Leipzig; Leipzig, Germany.

RNA Biology
|May 25, 2013
PubMed
Summary
This summary is machine-generated.

Researchers analyzed RNA sequencing data to find non-contiguously mapping reads in prokaryotes. They identified known cases of tRNA splicing and circular RNAs, plus novel archaeal ncRNAs, but most atypical reads remain unexplained.

Keywords:
RNA-seqcircular sRNAsself-splicing intronssplit tRNAs

More Related Videos

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Fecal (micro) RNA Isolation
05:35

Fecal (micro) RNA Isolation

Published on: October 28, 2020

Related Experiment Videos

Last Updated: May 11, 2026

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

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Fecal (micro) RNA Isolation
05:35

Fecal (micro) RNA Isolation

Published on: October 28, 2020

Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Prokaryotic transcripts typically map as continuous genomic regions.
  • Split reads, which map to discontiguous genomic loci, are often ignored in RNA sequencing analysis.
  • Known exceptions include tRNA splicing, circular RNAs in Archaea, and self-splicing introns.

Purpose of the Study:

  • To systematically screen published RNA sequencing datasets for non-contiguously mapping reads in prokaryotes.
  • To identify and characterize novel instances of unusual RNA processing events.
  • To investigate the origin and nature of atypical RNA sequencing reads.

Main Methods:

  • Reanalysis of existing RNA sequencing data.
  • Specific screening for reads mapping to discontiguous genomic loci.
  • Comparative analysis of identified reads with known RNA processing mechanisms.

Main Results:

  • Successfully recovered known cases of tRNA splicing and archaeal circular RNAs.
  • Discovered several novel archaeal non-coding RNAs (ncRNAs) associated with circularized products.
  • Identified only a few candidates in Eubacteria beyond known group I and group II introns.
  • Observed that most atypical reads did not clearly correspond to defined, processed RNA products.

Conclusions:

  • The study confirms and expands the known repertoire of non-contiguously mapping RNA species in Archaea.
  • The biological significance and origin of the majority of atypical prokaryotic RNA reads remain uncertain.
  • Further investigation is needed to determine if the diffuse background of atypical reads represents genuine biological products or technical artifacts.