Related Experiment Video

Updated: Mar 9, 2026

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

47.1K

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

Song-Yao Zhang1, Shao-Wu Zhang1, Lian Liu1

  • 1School of Automation, Northwestern Polytechnical University, Xi'an, Shaanxi, China.

Plos Computational Biology
|December 28, 2016
PubMed

Insights

This study introduces m6A-Driver, a new algorithm to predict genes and networks regulated by N6-methyladenosine (m6A) epigenetic modifications. It helps uncover complex regulatory circuits in gene expression.

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Bioinformatics

Background:

  • N6-methyladenosine (m6A) is the most common mRNA epigenetic modification in mammals, crucial for post-transcriptional gene regulation.
  • The precise regulatory mechanisms and functional networks of m6A remain largely unclear.
  • Understanding m6A's role is vital for deciphering gene regulation at the epitranscriptomic layer.

Purpose of the Study:

  • To develop m6A-Driver, an algorithm for predicting m6A-driven genes and their associated regulatory networks.
  • To unveil the functional circuits actively modulated by m6A methylation under specific biological conditions.
  • To provide insights into the dynamic interplay of m6A regulators.

Main Methods:

  • Integration of protein-protein interaction (PPI) networks with predicted differential m6A methylation sites from MeRIP-Seq data.
  • Application of the Random Walk with Restart (RWR) algorithm to identify m6A-driven genes.
  • Construction of context-specific m6A-driven networks for key m6A regulators (FTO, METTL3, METTL14, WTAP).

Main Results:

  • m6A-Driver robustly identifies m6A-driven genes with higher functional enrichment and differential expression compared to genes with differential m6A methylation.
  • Successfully constructed context-specific m6A-driven networks for known m6A (de)methylases.
  • Demonstrated the algorithm's efficiency in revealing condition-specific regulatory circuitry.

Conclusions:

  • m6A-Driver is an effective tool for dissecting m6A-mediated gene regulatory networks.
  • The findings illuminate the complex epitranscriptomic regulation driven by m6A.
  • Provides a foundation for further research into m6A's role in various biological processes.

More Related Videos

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.7K
Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV14:40

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

Published on: March 5, 2022

3.8K

Related Concept Videos

Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
9.8K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
7.6K
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.6K
Protein Networks02:26

Protein Networks

2.9K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
1.5K
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
798