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

Histone Modification02:32

Histone Modification

16.1K
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
16.1K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

9.5K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
9.5K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

14.8K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
14.8K
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

13.3K
One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
13.3K
RNA Interference01:23

RNA Interference

28.0K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
28.0K
RNA Splicing01:32

RNA Splicing

60.6K
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...
60.6K

You might also read

Related Articles

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

Sort by
Same author

Maraviroc attenuates inflammation-exacerbated cognitive and amyloid pathology in an early-stage Alzheimer's disease mouse model.

Translational psychiatry·2026
Same author

[Harmane ameliorates pulmonary fibrosis in mice by inhibiting transformation of lung fibroblasts into myofibroblasts].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica·2026
Same author

Charge-Energy Coupling Drives Ag<sub>6</sub> Nanocluster-Amine Self-Assembly.

The journal of physical chemistry letters·2026
Same author

Proteomic insights into azoospermia: protein differences in testicular tissue between non-obstructive and obstructive azoospermia patients.

Asian journal of andrology·2026
Same author

Targeting mGluR2/3 Signaling With LY341495 Restores Dentate Gyrus Function and Cognitive Performance in a Male Mouse Model of Alzheimer's Disease.

CNS neuroscience & therapeutics·2026
Same author

Spectrum-Effect Relationship-Based Analysis of Pneumonia Mixture Used for Pneumonia Treatment.

Biomedical chromatography : BMC·2026
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Feb 1, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

2.3K

Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data.

Xiao-Qin Zhang1, Jian-Hua Yang2

  • 1School of Medicine, South China University of Technology (SCUT), Guangzhou, China.

Methods in Molecular Biology (Clifton, N.J.)
|December 13, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces RMBase, a platform for analyzing RNA modifications from sequencing data. It provides tools to annotate, visualize, and study the functions of diverse epitranscriptomic marks.

Keywords:
EpitranscriptomeHigh-throughput sequencingN6-MethyladenosineRNA modificationSingle-nucleotide polymorphisms (SNPs)microRNA

More Related Videos

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV
14:40

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

Published on: March 5, 2022

3.8K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Related Experiment Videos

Last Updated: Feb 1, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

2.3K
Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV
14:40

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

Published on: March 5, 2022

3.8K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Over 100 RNA modifications exist, but their prevalence, regulation, and function are largely unknown.
  • High-throughput sequencing generates vast epitranscriptomic data requiring sophisticated analysis tools.

Purpose of the Study:

  • To present RMBase, a comprehensive platform and software suite for annotating, visualizing, and analyzing RNA modification sites.
  • To facilitate the functional study of diverse RNA modifications using epitranscriptomic data.

Main Methods:

  • Development of stand-alone software (modAnnotator, metaProfile) for RNA modification site annotation and visualization.
  • Construction of interactive web interfaces for analyzing various RNA modifications (m6A, Ψ, m5C, 2'-O-Me).
  • Integration of tools to analyze associations between RNA modifications, miRNA targets, and disease-related SNPs.

Main Results:

  • RMBase provides tools to annotate and visualize RNA modification sites and their prevalence.
  • Interactive web implementations allow exploration of diverse RNA modification atlases.
  • Web-based interfaces enable analysis of RNA modification associations with miRNA targets and SNPs.

Conclusions:

  • RMBase offers comprehensive interfaces and tools to aid in the analysis and functional study of RNA modification sites.
  • The platform is expected to accelerate research in the field of epitranscriptomics.