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

3.4K
3.4K
Epistasis Analysis01:09

Epistasis Analysis

5.0K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.0K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

7.4K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.4K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.1K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.1K
Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

9.8K
Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
9.8K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

3.0K
3.0K

You might also read

Related Articles

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

Sort by
Same author

The RMaP challenge of predicting RNA modifications by nanopore sequencing.

Communications chemistry·2025
Same author

Correction: Satam et al. Next-Generation Sequencing Technology: Current Trends and Advancements. <i>Biology</i> 2023, <i>12</i>, 997.

Biology·2024
Same author

Next-Generation Sequencing Technology: Current Trends and Advancements.

Biology·2023
Same author

Transport Granules Bound with Nuclear Cap Binding Protein and Exon Junction Complex Are Associated with Microtubules and Spatially Separated from eIF4E Granules and P Bodies in Human Neuronal Processes.

Frontiers in molecular biosciences·2018
Same author

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif.

Frontiers in molecular neuroscience·2017
Same author

Preparation of Aplysia sensory-motor neuronal cell cultures.

Journal of visualized experiments : JoVE·2009

Related Experiment Video

Updated: Jul 5, 2025

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

5.1K

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation.

Kandarp Joshi1, Dan O Wang1,2,3

  • 1Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan.

Briefings in Bioinformatics
|January 25, 2024
PubMed
Summary

Scientists developed epidecodeR, an R package to link epigenetic marks (epi-marks) to gene expression. This tool helps explore how DNA and RNA modifications influence biological processes and predict treatment effectiveness.

Keywords:
R packagechemical modificationsdata visualizationgene expressiongene regulationshiny application

More Related Videos

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.4K
A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure
09:06

A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure

Published on: October 24, 2018

10.8K

Related Experiment Videos

Last Updated: Jul 5, 2025

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

5.1K
Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.4K
A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure
09:06

A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure

Published on: October 24, 2018

10.8K

Area of Science:

  • Epigenetics and Epitranscriptomics
  • Bioinformatics and Computational Biology
  • Gene Regulation

Background:

  • High-throughput sequencing generates vast epigenomic and epitranscriptomic data.
  • Existing in silico methods identify and quantify modification sites but struggle to link them to gene expression.
  • A critical gap exists in connecting specific epigenetic modifications ('epi-marks') to gene expression within biological contexts.

Purpose of the Study:

  • To develop a computational tool, epidecodeR, to facilitate the exploration of relationships between epigenomic/epitranscriptomic status and gene expression.
  • To enable biologists to rapidly assess the potential influence of 'epi-marks' on gene expression responses.
  • To provide a user-friendly R package for analyzing large-scale epigenetic datasets.

Main Methods:

  • Implementation of epidecodeR in R, utilizing cumulative distribution function and differential gene expression analysis.
  • Grouping genes based on the number of associated 'epi-marks' to evaluate statistical significance.
  • Application of the tool to analyze histone modifications (H3K9ac, H3K27ac) and N6-methyl-adenosine (m6A) modifications.

Main Results:

  • epidecodeR successfully predicted the role of H3K9ac and H3K27ac in gene expression following deacetylase knockdown.
  • The tool demonstrated utility in linking N6-methyl-adenosine modifications to gene expression after reader protein knockout.
  • epidecodeR was applied to investigate the effects of FTO inhibitors and histone modifications in animal models of drug abuse.

Conclusions:

  • epidecodeR is a valuable tool for biologists to rapidly survey and understand the impact of epigenomic and epitranscriptomic modifications on gene expression.
  • The package aids in connecting specific 'epi-marks' to cellular and biological processes, accelerating research in life sciences.
  • epidecodeR offers a novel approach to explore potential therapeutic targets and treatment efficacies, as demonstrated in drug abuse studies.