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. 2025 Apr 14;6(4):101228.
doi: 10.1016/j.xplc.2024.101228. Epub 2024 Dec 20.

PlantEMS: A comprehensive database of epigenetic modification sites across multiple plant species

Fuying Dao  1 , Xueqin Xie  2 , Hongqi Zhang  2 , Zhengxing Guan  2 , Changchun Wu  2 , Wei Su  2 , Yijie Wei  2 , Feitong Hong  2 , Xinwei Luo  2 , Sijia Xie  2 , Hongyan Lai  3 , Dong Gao  2 , Yuhe Yang  2 , Yang Zhang  4 , Lin Ning  5 , Shihao Li  2 , Yuduo Hao  2 , Benjamin Lebeau  1 , Crystal Chia Yin Ling  1 , Jian Huang  2 , Melissa Jane Fullwood  6 , Hao Lin  7 , Hao Lv  8
Affiliations

PlantEMS: A comprehensive database of epigenetic modification sites across multiple plant species

Fuying Dao et al. Plant Commun. .

Abstract

In summary, PlantEMS is designed to advance plant epigenetics research by providing a comprehensive repository of multi-omics and multi-modification data. This resource enables detailed investigations into the epigenetic regulatory mechanisms underlying essential plant traits and responses, potentially informing innovative strategies for crop management, monitoring, and development.

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Figures

Figure 1
Figure 1
Overview of PlantEMS PlantEMS compiles experimentally confirmed epigenetic modification datasets from published literature and existing databases, covering 54 plant species. PlantEMS includes 13 009 568 DNA modification sites of four types from six plants, 33 337 RNA modification sites of 28 types from 33 plants, and 132 232 PTM sites of 25 types from 28 plants. Additionally, PlantEMS integrates 12 omics-type-species prediction tools.
See this image and copyright information in PMC

References

    1. Allis C.D., Jenuwein T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 2016;17:487–500. doi: 10.1038/nrg.2016.59. - DOI - PubMed
    1. Bulgakov V.P. Chromatin modifications and memory in regulation of stress-related polyphenols: finding new ways to control flavonoid biosynthesis. Crit. Rev. Biotechnol. 2024;44:1478–1494. doi: 10.1080/07388551.2024.2336529. - DOI - PubMed
    1. Dao F.Y., Lv H., Yang Y.H., Zulfiqar H., Gao H., Lin H. Computational identification of N6-methyladenosine sites in multiple tissues of mammals. Comput. Struct. Biotechnol. J. 2020;18:1084–1091. doi: 10.1016/j.csbj.2020.04.015. - DOI - PMC - PubMed
    1. Lang X., Yu C., Shen M., Gu L., Qian Q., Zhou D., Tan J., Li Y., Peng X., Diao S., et al. PRMD: an integrated database for plant RNA modifications. Nucleic Acids Res. 2024;52:D1597–D1613. doi: 10.1093/nar/gkad851. - DOI - PMC - PubMed
    1. Lv H., Zhang Z.M., Li S.H., Tan J.X., Chen W., Lin H. Evaluation of different computational methods on 5-methylcytosine sites identification. Briefings Bioinf. 2020;21:982–995. doi: 10.1093/bib/bbz048. - DOI - PubMed

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