DNA sequence sets the destination of spontaneous epimutations in plants
- 1New Laboratory of Pattern Recognition (NLPR), State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academ
Abstract
Plant genomes gain and lose cytosine methylation spontaneously, far faster than DNA mutates, and these epimutations are inherited. The genome is thought to set a steady state around which methylation fluctuates. Here we show that this steady state, the set point, is written in the DNA of each CG site: REED, a deep-learning model trained on one methylome, reads it. In pedigrees of seven Arabidopsis thaliana accessions, gains concentrated at high set points and losses at low ones, and the equilibrium implied by their rates matched the set point, tracking it within genes. Stress sped epimutation but barely shifted its destination. The set point predicted germline epimutations in rice and changes accumulated in the wild and in a 330-year-old tree. Its rules, cooperation between nearby CG sites and transcription-factor motifs that lower methylation, are shared across flowering plants, so a genome and one methylome reveal where epigenetic variation is heading.
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BibTeX
@misc{wang2026sequence,
title = {{DNA sequence sets the destination of spontaneous epimutations in plants}},
author = {D. Wang and J. Jin and J. Qiao and L. Wei and Q. Liu},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.21.760629},
url = {https://www.biorxiv.org/content/10.64898/2026.10.21.760629v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - DNA sequence sets the destination of spontaneous epimutations in plants
AU - D. Wang
AU - J. Jin
AU - J. Qiao
AU - L. Wei
AU - Q. Liu
PY - 2026
DA - 2026/10/21
PB - bioRxiv
DO - 10.64898/2026.10.21.760629
UR - https://www.biorxiv.org/content/10.64898/2026.10.21.760629v1
AB - Plant genomes gain and lose cytosine methylation spontaneously, far faster than DNA mutates, and these epimutations are inherited. The genome is thought to set a steady state around which methylation fluctuates. Here we show that this steady state, the set point, is written in the DNA of each CG site: REED, a deep-learning model trained on one methylome, reads it. In pedigrees of seven Arabidopsis thaliana accessions, gains concentrated at high set points and losses at low ones, and the equilibrium implied by their rates matched the set point, tracking it within genes. Stress sped epimutation but barely shifted its destination. The set point predicted germline epimutations in rice and changes accumulated in the wild and in a 330-year-old tree. Its rules, cooperation between nearby CG sites and transcription-factor motifs that lower methylation, are shared across flowering plants, so a genome and one methylome reveal where epigenetic variation is heading.
ER -