---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20479'
abstract:
- lang: eng
text: 'Genetic variation is generally regarded as a prerequisite for evolution.
In principle, epigenetic information inherited independently of DNA sequence can
also enable evolution, but whether this occurs in natural populations is unknown.
Here we show that single-nucleotide and epigenetic gene body DNA methylation (gbM)
polymorphisms explain comparable amounts of expression variance in Arabidopsis
thaliana populations. We genetically demonstrate that gbM regulates
transcription, and we identify and genetically validate many associations between
gbM polymorphism and the variation of complex traits: fitness under heat and drought,
flowering time and accumulation of diverse minerals. Epigenome-wide association
studies pinpoint trait-relevant genes with greater precision than genetic association
analyses, probably due to reduced linkage disequilibrium between gbM variants.
Finally, we identify numerous associations between gbM epialleles and diverse
environmental conditions in native habitats, suggesting that gbM facilitates adaptation.
Overall, our results indicate that epigenetic methylation variation fundamentally
shapes phenotypic diversity in a natural population.'
acknowledgement: We thank P. Baduel and V. Colot for sharing SV data, A. Muyle for
gbM conservation data and X. Feng, C. Dean, E. Coen and Zilberman lab members for
constructive comments on the paper. This work was supported by a European Research
Council grant (725746) to D.Z., LUMS Startup grant (STG-188) to Z.S. and US National
Science Foundation grant (MCB-2334561) to H.R. This study would not have been possible
without Arabidopsis 1001 genome, methylome and transcriptome resources. Open access
funding provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Zaigham
full_name: Shahzad, Zaigham
last_name: Shahzad
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Gaëlle
full_name: Cassin-Ross, Gaëlle
last_name: Cassin-Ross
- first_name: Hatem
full_name: Rouached, Hatem
last_name: Rouached
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Shahzad Z, Hollwey E, Moore JD, et al. Gene body methylation regulates gene
expression and mediates phenotypic diversity in natural Arabidopsis populations.
Nature Plants. 2025;11:2084-2099. doi:10.1038/s41477-025-02108-4
apa: Shahzad, Z., Hollwey, E., Moore, J. D., Choi, J., Cassin-Ross, G., Rouached,
H., … Zilberman, D. (2025). Gene body methylation regulates gene expression and
mediates phenotypic diversity in natural Arabidopsis populations. Nature Plants.
Springer Nature. https://doi.org/10.1038/s41477-025-02108-4
chicago: Shahzad, Zaigham, Elizabeth Hollwey, Jonathan D. Moore, Jaemyung Choi,
Gaëlle Cassin-Ross, Hatem Rouached, Matthew Richard Robinson, and Daniel Zilberman.
“Gene Body Methylation Regulates Gene Expression and Mediates Phenotypic Diversity
in Natural Arabidopsis Populations.” Nature Plants. Springer Nature, 2025.
https://doi.org/10.1038/s41477-025-02108-4.
ieee: Z. Shahzad et al., “Gene body methylation regulates gene expression
and mediates phenotypic diversity in natural Arabidopsis populations,” Nature
Plants, vol. 11. Springer Nature, pp. 2084–2099, 2025.
ista: Shahzad Z, Hollwey E, Moore JD, Choi J, Cassin-Ross G, Rouached H, Robinson
MR, Zilberman D. 2025. Gene body methylation regulates gene expression and mediates
phenotypic diversity in natural Arabidopsis populations. Nature Plants. 11, 2084–2099.
mla: Shahzad, Zaigham, et al. “Gene Body Methylation Regulates Gene Expression and
Mediates Phenotypic Diversity in Natural Arabidopsis Populations.” Nature Plants,
vol. 11, Springer Nature, 2025, pp. 2084–99, doi:10.1038/s41477-025-02108-4.
short: Z. Shahzad, E. Hollwey, J.D. Moore, J. Choi, G. Cassin-Ross, H. Rouached,
M.R. Robinson, D. Zilberman, Nature Plants 11 (2025) 2084–2099.
corr_author: '1'
date_created: 2025-10-16T13:11:21Z
date_published: 2025-09-12T00:00:00Z
date_updated: 2025-12-01T14:59:10Z
day: '12'
ddc:
- '580'
department:
- _id: MaRo
- _id: DaZi
doi: 10.1038/s41477-025-02108-4
ec_funded: 1
external_id:
isi:
- '001570197600001'
pmid:
- '40940427'
file:
- access_level: open_access
checksum: 6a3f6cffdc934b8a2015c3c247f5a92a
content_type: application/pdf
creator: dernst
date_created: 2025-10-23T11:13:58Z
date_updated: 2025-10-23T11:13:58Z
file_id: '20524'
file_name: 2025_NaturePlants_Shahzad.pdf
file_size: 7746662
relation: main_file
success: 1
file_date_updated: 2025-10-23T11:13:58Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 2084-2099
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gene body methylation regulates gene expression and mediates phenotypic diversity
in natural Arabidopsis populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2025'
...