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Epigenetic Regulation

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...

Epigenetic Regulation

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.

Epigenetic Regulation

Epigenetic Regulation

Types of RNA

Types of RNA

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...

Types of RNA

Types of RNA

Overview
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 the regulation of 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...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

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Related Experiment Video

Updated: Mar 26, 2026

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Published on: September 7, 2017

Mobile small RNAs regulate genome-wide DNA methylation.

Mathew G Lewsey¹, Thomas J Hardcastle², Charles W Melnyk²

¹Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;

Proceedings of the National Academy of Sciences of the United States of America

|January 21, 2016

Summary

Mobile small RNAs (sRNAs) from plant shoots mediate transcriptional gene silencing in roots, establishing RNA-directed DNA methylation (RdDM) predominantly in non-CG contexts. This mobile sRNA-dependent RdDM pathway impacts transposable elements and gene expression across different plant accessions.

Keywords:

RNA-directed DNA methylation plant grafting small RNA transcriptional gene silencing transposable element

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DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

Published on: September 16, 2019

Area of Science:

Plant molecular biology
Epigenetics
RNA biology

Background:

RNA silencing regulates gene expression, transposable elements, and viral defense using small RNAs (sRNAs).
Transcriptional gene silencing involves 24-nt sRNAs and RNA-directed DNA methylation (RdDM) in CG, CHG, and CHH contexts.
Previously, 24-nt sRNAs were shown to move from shoot to root in Arabidopsis thaliana, mediating DNA methylation.

Purpose of the Study:

To investigate the role of mobile sRNAs in mediating RNA-directed DNA methylation (RdDM) in root tissues.
To determine the DNA sequence contexts and pathways involved in mobile sRNA-dependent RdDM.
To identify genes and transposable elements (TEs) affected by mobile sRNA-dependent DNA methylation.

Main Methods:

Analysis of DNA methylation patterns in wild-type and mutant Arabidopsis thaliana lacking specific small RNA pathways.
Grafting experiments to study sRNA movement and epigenetic effects between different accessions.
Transcriptome analysis to identify genes regulated by mobile sRNAs and DNA methylation.

Main Results:

Mobile sRNAs from shoots induce RdDM at thousands of loci in root tissues, primarily in non-CG contexts.
Mobile sRNA-dependent non-CG methylation relies on DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3.
A dicer-like 2, 3, 4 triple mutant showed loss of DNA methylation in specific TE superfamilies.
Mobile sRNAs influence the expression of a subset of root genes and can mediate de novo DNA methylation across graft unions.

Conclusions:

Mobile sRNAs are key mediators of systemic transcriptional gene silencing and epigenetic regulation in plants.
The mobile sRNA-dependent RdDM pathway primarily targets non-CG DNA methylation, impacting TEs and gene expression.
sRNA-mediated epigenetic effects can occur across graft unions, influencing genome-wide methylation patterns in recipient tissues.