PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation

PICKLE (PKL) encodes a chromodomain helicase DNA-binding 3-type chromatin remodeling factor in Arabidopsis. Although PKL is known to influence plant development and environmental responses, its role in regulating chromatin states remains unclear. Using ChIP-seq with an endogenous PKL antibody, we identified 3534 high-confidence PKL-binding sites across the genome. PKL occupancy significantly overlapped with TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs), PHYTOCHOME INTERACTING FACTORs (PIFs), and ELONGATED HYPOCOTYL 5 (HY5) near the target gene transcription start site, and binding at shared targets decreased in the corresponding mutants, indicating that these transcription factors facilitate PKL recruitment. PKL-bound loci were enriched for H3K4me2 and H3K4me3, and loss of PKL reduced H3K4me2 levels. PKL also interacts with WDR5A and facilitates its chromatin occupancy at shared loci, which may contribute to H3K4 methylation regulation. Moreover, PKL-associated regions displayed spatial clustering coordinated with PKL and its transcription factor partners, reflecting chromatin organization at specific genes, a feature conserved for PKL and TCP homologs in Marchantia. Overall, our findings reveal that PKL promotes H3K4me2 levels, establishes a permissive chromatin environment, and orchestrates the spatial clustering of its genomic targets.

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Publication Details

Journal
Nucleic Acids Research
Published
2025-11-26
DOI
https://doi.org/10.1093/nar/gkaf1376
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
0.00

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article

PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation

Xing Wang Deng, Huijie Wang, Rongcheng Lin, William Terzaghi et al.
Nucleic Acids Research
Plant Molecular Biology Research
article

PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation

Xing Wang Deng, Huijie Wang, Rongcheng Lin, William Terzaghi, Danmeng Zhu, Yanjun Jing, Miao Song, Kai He, Yubo Wang, Bo Xu, Tao Ma, Yuqiu Wang
article en

Abstract

PICKLE (PKL) encodes a chromodomain helicase DNA-binding 3-type chromatin remodeling factor in Arabidopsis. Although PKL is known to influence plant development and environmental responses, its role in regulating chromatin states remains unclear. Using ChIP-seq with an endogenous PKL antibody, we identified 3534 high-confidence PKL-binding sites across the genome. PKL occupancy significantly overlapped with TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs), PHYTOCHOME INTERACTING FACTORs (PIFs), and ELONGATED HYPOCOTYL 5 (HY5) near the target gene transcription start site, and binding at shared targets decreased in the corresponding mutants, indicating that these transcription factors facilitate PKL recruitment. PKL-bound loci were enriched for H3K4me2 and H3K4me3, and loss of PKL reduced H3K4me2 levels. PKL also interacts with WDR5A and facilitates its chromatin occupancy at shared loci, which may contribute to H3K4 methylation regulation. Moreover, PKL-associated regions displayed spatial clustering coordinated with PKL and its transcription factor partners, reflecting chromatin organization at specific genes, a feature conserved for PKL and TCP homologs in Marchantia. Overall, our findings reveal that PKL promotes H3K4me2 levels, establishes a permissive chromatin environment, and orchestrates the spatial clustering of its genomic targets.

Nucleic Acids ResearchVol. 53(22)
Wilkes University (US), Chinese Academy of Sciences (CN), Peking University (CN), Sichuan University (CN), EES Research (United Kingdom) (GB), Ministry of Agriculture (EE), Institute of Forestry (RS), Ministry of Agriculture (ID), Czech Academy of Sciences, Institute of Botany (CZ), Beijing Academy of Agricultural and Forestry Sciences (CN), Ministry of Agriculture and Rural Affairs (CN), Xihu Institute of Electronic Research (CN), Institute of Botany (CN), Center for Life Sciences (CN), Weifang University (CN)
National Natural Science Foundation of China, Beijing Academy of Agricultural and Forestry Sciences, Peking University, Ministry of Agriculture and Rural Affairs of the People's Republic of China
Openalex Percentile: Top 72%
Plant Molecular Biology Research
DOIOpen Access PDFOpenAlex
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