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

Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
RNA-seq03:21

RNA-seq

11.5K
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...
11.5K
Leaky Scanning02:28

Leaky Scanning

5.5K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.5K
Types of RNA01:20

Types of RNA

8.6K
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
8.6K

You might also read

Related Articles

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

Sort by
Same author

Single-cell analysis reveals the cellular and transcriptional heterogeneity of the normal pediatric thyroid.

Frontiers in endocrinology·2026
Same author

DNA Methylation-Based Risk Stratification and Classification of Pediatric Thyroid Carcinoma.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same author

Afirma genomic sequencing classifier performance in young patients with cytologically indeterminate thyroid nodules.

The Journal of clinical endocrinology and metabolism·2026
Same author

Modified tumor uptake and biodistribution of nanoparticles coated with small extracellular vesicle membranes derived from distinct tumor cell lines.

International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group·2026
Same author

<i>KEAP1</i> mutations activate the NRF2 pathway to drive cell growth and migration, and attenuate drug response in thyroid cancer.

Frontiers in oncology·2026
Same author

The Year in Thyroidology 2025-Basic Science, Clinical Science, Surgical Science.

Thyroid : official journal of the American Thyroid Association·2025
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Dec 13, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.0K

Decoding the epitranscriptional landscape from native RNA sequences.

Piroon Jenjaroenpun1, Thidathip Wongsurawat1, Taylor D Wadley1

  • 1Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.

Nucleic Acids Research
|July 26, 2020
PubMed
Summary
This summary is machine-generated.

A new bioinformatics tool, ELIGOS, detects RNA modifications directly from native RNA sequencing data. This method overcomes limitations of traditional epitranscriptomics, enabling accurate identification of methylation sites in various RNA types.

More Related Videos

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
11:04

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

10.3K
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

59.1K

Related Experiment Videos

Last Updated: Dec 13, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.0K
RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
11:04

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

10.3K
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

59.1K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Traditional epitranscriptomics uses antibody or chemical methods for RNA modification detection, which are labor-intensive and prone to artifacts.
  • Direct RNA sequencing with Oxford Nanopore Technologies (ONT) offers potential for base modification detection, but modifications appear as sequencing errors.

Purpose of the Study:

  • To develop a bioinformatics tool for accurate detection of RNA modifications directly from native RNA sequencing data.
  • To overcome the limitations of traditional epitranscriptomics and experimental artifacts.

Main Methods:

  • Development of ELIGOS (epitranscriptional landscape inferring from glitches of ONT signals), a bioinformatics tool utilizing % Error of Specific Bases (%ESB) differences in ONT native RNA sequencing.
  • Application of ELIGOS to rRNA and mRNA from various organisms (E. coli, yeast, human) and cell lines, using synthetic modified RNA and background error models for reference.
  • Differential analysis of ELIGOS to study RNA methyltransferase impact by comparing wild-type and knockout cells.

Main Results:

  • ELIGOS accurately predicts known RNA methylation sites in rRNAs (AUC > 0.93) and identifies the DRACH/RRACH motif.
  • The tool successfully identified the DRACH motif in mRNA from human cell lines at single-base resolution.
  • Differential analysis revealed the impact of RNA m6A methyltransferase in yeast and mouse cells.

Conclusions:

  • ELIGOS is a robust bioinformatics software package for uncovering native RNA modifications with high accuracy and single-base resolution.
  • The developed tool advances epitranscriptomics by enabling direct detection of RNA modifications, bypassing labor-intensive traditional methods.
  • ELIGOS facilitates the study of RNA modification dynamics and the impact of methyltransferases across different species and RNA types.