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Predicting protein synergistic effect in Arabidopsis using epigenome profiling

Author

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  • Chih-Hung Hsieh

    (Academia Sinica)

  • Ya-Ting Sabrina Chang

    (Academia Sinica)

  • Ming-Ren Yen

    (Academia Sinica)

  • Jo-Wei Allison Hsieh

    (Academia Sinica)

  • Pao-Yang Chen

    (Academia Sinica)

Abstract

Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 histone modifications in Arabidopsis, offering three key functionalities. Firstly, QHistone employs machine learning to predict the epigenomic profile of a query protein, characterized by its most associated histone modifications, and uses these modifications to infer the protein’s role in transcriptional regulation. Secondly, it predicts synergistic regulatory activities between two proteins by comparing their profiles. Lastly, it detects previously unexplored co-regulating protein pairs by screening all known proteins. QHistone accurately identifies histone modifications associated with specific known proteins, and allows users to computationally validate their results using gene expression data from various plant tissues. These functions demonstrate an useful approach to utilizing epigenome data for gene regulation analysis, making QHistone a valuable resource for the scientific community ( https://qhistone.paoyang.ipmb.sinica.edu.tw ).

Suggested Citation

  • Chih-Hung Hsieh & Ya-Ting Sabrina Chang & Ming-Ren Yen & Jo-Wei Allison Hsieh & Pao-Yang Chen, 2024. "Predicting protein synergistic effect in Arabidopsis using epigenome profiling," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53565-y
    DOI: 10.1038/s41467-024-53565-y
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    References listed on IDEAS

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    1. Xiaochang Yin & Francisco J. Romero-Campero & Pedro de Los Reyes & Peng Yan & Jing Yang & Guangmei Tian & XiaoZeng Yang & Xiaorong Mo & Shuangshuang Zhao & Myriam Calonje & Yue Zhou, 2021. "H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Cuijun Zhang & Xuan Du & Kai Tang & Zhenlin Yang & Li Pan & Peipei Zhu & Jinyan Luo & Yuwei Jiang & Hui Zhang & Huafang Wan & Xingang Wang & Fengkai Wu & W. Andy Tao & Xin-Jian He & Heng Zhang & Ray A, 2018. "Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
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