The mirage of DNA methylation in transcriptional regulation of plants
Abstract
Cytosine methylation plays an important role in the regulation of gene expression in plants." Some iteration of this statement can be found in most papers centered on plant epigenetics and has become a widely accepted textbook claim. However, our generalized understanding of how DNA methylation exerts control over transcription is now challenged by observations demonstrating that transcriptional levels of most genes are unresponsive to DNA methylation changes. On a genome-wide scale, associations between DNA methylation and transcription are usually statistically weak.Even when correlations are found, the cause and effect can be difficult to identify, as methylation changes sometimes follow rather than precede transcriptional changes.While a growing number of studies explore a possible connection between differentially expressed genes (DEGs) and differentially methylated genes (DMGs), we demonstrate here that DEG-DMG overlaps are often significantly smaller than what could be expected by chance. This indicates that, contrary to expectations, changes in DNA methylation and changes in transcription sometimes avoid one another.Here, we discuss such observations and their implications for the hypothesis of a widespread control of gene expression directly by DNA methylation. While there are well-documented examples where DNA methylation regulates transcription, we argue that such cases represent a minority of genes, and we opine that approaches of reverse epigenetics are therefore unlikely to find broad application in breeding.
Related
- Transcriptional Regulation of the Meiotic Cohesin Subunit RAD21L by Methylation of Two CpG Islands in Its Promoter and Characterization of Its Interactions with Histones
- Simultaneous X-chromosome inactivation and tissue-/cell-type-specific DNA methylation in the transcriptional regulatory region of the X-linked recessive disease gene OTC.
- Urinary TAGMe methylation enables preoperative risk stratification and reveals enhancer‑mediated regulation in urothelial carcinoma
- cBAF drives AR-V7 expression through regulation of transcriptional termination in castration-resistant prostate cancer
- IPF distal lung epithelial cells acquire a DNA methylation signature consistent with activation of basal cell transcriptional programs
BibTeX
@article{civan2026mirage,
title = {{The mirage of DNA methylation in transcriptional regulation of plants}},
author = {Peter Civan and Iris Sammarco and Meriem Banouh},
journal = {Plant Genome},
year = {2026},
month = oct,
doi = {10.1002/tpg2.70208},
url = {https://hal.inrae.fr/hal-05784016v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - The mirage of DNA methylation in transcriptional regulation of plants
AU - Peter Civan
AU - Iris Sammarco
AU - Meriem Banouh
PY - 2026
DA - 2026/10/07
JO - Plant Genome
DO - 10.1002/tpg2.70208
UR - https://hal.inrae.fr/hal-05784016v1
AB - Cytosine methylation plays an important role in the regulation of gene expression in plants." Some iteration of this statement can be found in most papers centered on plant epigenetics and has become a widely accepted textbook claim. However, our generalized understanding of how DNA methylation exerts control over transcription is now challenged by observations demonstrating that transcriptional levels of most genes are unresponsive to DNA methylation changes. On a genome-wide scale, associations between DNA methylation and transcription are usually statistically weak.Even when correlations are found, the cause and effect can be difficult to identify, as methylation changes sometimes follow rather than precede transcriptional changes.While a growing number of studies explore a possible connection between differentially expressed genes (DEGs) and differentially methylated genes (DMGs), we demonstrate here that DEG-DMG overlaps are often significantly smaller than what could be expected by chance. This indicates that, contrary to expectations, changes in DNA methylation and changes in transcription sometimes avoid one another.Here, we discuss such observations and their implications for the hypothesis of a widespread control of gene expression directly by DNA methylation. While there are well-documented examples where DNA methylation regulates transcription, we argue that such cases represent a minority of genes, and we opine that approaches of reverse epigenetics are therefore unlikely to find broad application in breeding.
SN - 1940-3372
SN - 1940-3372
ER -