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Development of Chromatin Immunoprecipitation for the Analysis of Histone Modifications in Red Macroalga Neopyropia yezoensis (Rhodophyta)

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Abstract

Epigenetic regulation by histone modification can activate or repress transcription through changes in chromatin dynamics and regulates development and the response to environmental signals in both animals and plants. Chromatin immunoprecipitation (ChIP) is an indispensable tool to identify histones with specific post-translational modifications. The lack of a ChIP technique for macroalgae has hindered understanding of the role of histone modification in the expression of genes in this organism. In this study, a ChIP method with several modifications, based on existing protocols for plant cells, has been developed for the red macroalga, Neopyropia yezoensis, that consists of a heterogeneous alternation of macroscopic leaf-like gametophytes and microscopic filamentous sporophytes. ChIP method coupled with qPCR enables the identification of a histone mark in generation-specific genes from N. yezoensis. The results indicate that acetylation of histone H3 at lysine 9 in the 5′ flanking and coding regions from generation-specific genes was maintained at relatively high levels, even in generation-repressed gene expression. The use of this ChIP method will contribute significantly to identify the epigenetic regulatory mechanisms through histone modifications that control a variety of biological processes in red macroalgae.

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Data Availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

We wish to thank Drs. Katsutoshi Arai, Takafumi Fujimoto, and Toshiya Nishimura (Hokkaido University, Japan) for kindly providing the LightCycler 480 system.

Funding

This work was supported by the Grant-in-Aid for Young Scientists [Grant Number 19K15907 and 22K05779 to TU] from the Japan Society for the Promotion of Science.

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  1. Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan

    Shinnosuke Ueda, Hiroyuki Mizuta & Toshiki Uji

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  1. Shinnosuke Ueda
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  2. Hiroyuki Mizuta
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  3. Toshiki Uji
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Correspondence to Toshiki Uji.

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Ueda, S., Mizuta, H. & Uji, T. Development of Chromatin Immunoprecipitation for the Analysis of Histone Modifications in Red Macroalga Neopyropia yezoensis (Rhodophyta). Mol Biotechnol 65, 590–597 (2023). https://doi.org/10.1007/s12033-022-00562-5

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