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

Conserved Binding Sites01:49

Conserved Binding Sites

5.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.1K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

9.4K
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...
9.4K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

14.7K
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,...
14.7K
Ligand Binding Sites02:40

Ligand Binding Sites

14.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.9K
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 Splicing01:32

RNA Splicing

60.5K
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...
60.5K

You might also read

Related Articles

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

Sort by
Same author

USP22 deficiency in melanoma mediates resistance to T cells through IFNγ-JAK1-STAT1 signal axis.

Molecular therapy : the journal of the American Society of Gene Therapy·2021
Same author

Prognostic value of eight immune gene signatures in pancreatic cancer patients.

BMC medical genomics·2021
Same author

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters.

Journal of molecular biology·2021
Same author

Generation of an induced pluripotent stem cell line from a Chinese Han infant with floating-harbor syndrome accompanied with dilated cardiomyopathy.

Stem cell research·2021
Same author

Identification of Key Histone Modifications and Their Regulatory Regions on Gene Expression Level Changes in Chronic Myelogenous Leukemia.

Frontiers in cell and developmental biology·2021
Same author

DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism.

Nucleic acids research·2021

Related Experiment Video

Updated: Jan 25, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K

iRNAD: a computational tool for identifying D modification sites in RNA sequence.

Zhao-Chun Xu1,2, Peng-Mian Feng3, Hui Yang2

  • 1Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.

Bioinformatics (Oxford, England)
|May 12, 2019
PubMed
Summary

A new computational model, iRNAD, accurately predicts dihydrouridine (D) modification sites in RNA. This tool aids in understanding D

More Related Videos

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
07:35

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

1.1K
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K

Related Experiment Videos

Last Updated: Jan 25, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K
Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
07:35

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

1.1K
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Dihydrouridine (D) is a prevalent RNA modification impacting nucleotide flexibility.
  • Elevated D levels are observed in cancerous tissues, highlighting its clinical relevance.
  • Efficient detection of D modification sites is crucial for functional studies.

Purpose of the Study:

  • To develop a computational predictor for identifying D modification sites in RNA sequences.
  • To provide a robust and reliable tool for RNA modification analysis.

Main Methods:

  • RNA sequences from five species were encoded using nucleotide chemical properties and density.
  • A Support Vector Machine (SVM) algorithm was employed for classification.
  • Model performance was rigorously evaluated using jackknife cross-validation.

Main Results:

  • The iRNAD predictor achieved an overall accuracy of 96.18%.
  • The model demonstrated a high Area Under the Curve (AUC) of 0.9839.
  • Extensive validation confirmed the predictor's robustness and reliability.

Conclusions:

  • The iRNAD predictor offers an efficient and accurate method for identifying D modification sites.
  • The developed web-server provides accessible computational support for researchers.
  • This tool facilitates further investigation into the functional roles of D modification in RNA.