Dynamic histone modification signatures coordinate developmental programs in strawberry fruit ripening

Abstract

Chromatin structure plays a critical role in the regulation of dynamic gene expression in response to different developmental and environmental cues, but as yet their involvement in fruit ripening is not well understood. Here, we profile seven histone modifications in the woodland strawberry (Fragaria vesca) genome and analyze the histone modification signatures during ripening. Collectively, segments painted by the seven marks cover ∼85% of the woodland strawberry genome. We report an eight-state chromatin structure model of the woodland strawberry based on the above histone marks, which reveals a diverse chromatin environment closely associated with transcriptional apparatus. Upon this model we build a chromatin-centric annotation to the strawberry genome. Expression of many genes essential for fruit ripening, such as abscisic acid catabolism, anthocyanin accumulation and fruit softening, are associated with shifts of active genic states and polycomb-associated chromatin states. Particularly, the expression levels of ripening-related genes are well correlated with histone acetylation, indicating a regulatory role of histone acetylation in strawberry ripening. Our identification of the chromatin states underpinning genome expression during fruit ripening not only elucidates the coordination of different pathways of morphological and metabolic development but also provides a framework to understand the signals that regulate fruit ripening.

Acknowledgements

We thank Dr Juyou Wu, Dr Jia-Xing Yue, Dr Sihai Yang and Dr Long Wang for critical reading and comments on the manuscript. This work was supported by the National Natural Science Foundation of China (31972382), the Key Research and Development Program (Modern Agriculture) of Jiangsu Province, China (BE2022381), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author contributions

Q.P., S.G., Y.Z, Q.Q., and X.H. performed the experiments. Q.P., T.G., and J.D. conducted bioinformatic analysis. F.W. and H.W. had input in project development and writing. T.G. and Y.L. conceived the project and designed the data presentation and manuscript writing. T.G. and Q.P. wrote the manuscript with contributions from all authors.

Data availability

The sequencing data used in this study, the corresponding processed data files for visualization, and the genomic occurrence of the eight chromatin states are available from Gene Expression Omnibus under GSE208640 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208640).

Conflict of interests

None declared.

Supplementary data

Supplementary data are available at Horticulture Research online.

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