Dynamic profiles of DNA methylation and the interaction with histone acetylation during fiber cell initiation of Gossypium hirsutum

Abstract Background Fiber, as the main product of cotton, provides main raw material for the textile industry. Many key factors have been revealed a significant role in fiber cell development including Myb proteins, phytohormones, fatty acid metabolites, and epigenetic modifications. DNA methylation is one of the important epigenetic modifications to regulate plant development and responses to abiotic or biotic stimuli. In general, DNA methylation consisting of 5mC and 6mA regulates the chromatin structure and gene transcription to affect plant development, however, the detailed role and underlying mechanism of DNA methylation in the fiber development of cotton are yet vague. Results Here, systematical study of the 5mC and 6mA DNA methylation profiles during the fiber initiation period of Xu142 and its glabrous mutant Xu142fl represented a clear alteration of global DNA methylation associated with fiber cell initiation. Then, the genome-wide identification of genes responsible for methylation regulation at the fifth carbon of cytosine and the sixth carbon of adenine of DNA was operated in Gossypium hirsutum. As a result, 13, 10, 6, and 17 genes were identified for 5mC methylation, 5mC demethylation, 6mA methylation, and 6mA demethylation, respectively. We then investigated the tissue expression pattern of all these genes, and some genes showed higher expression levels in fiber initiation, among which some displayed a significant change in transcription between Xu142 and Xu142fl. The possible interaction between histone acetylation and DNA methylation in fiber initiation through in vitro culture was studied by dot blot, and the results showed that repressed histone deacetylation by Trichostatin A (TSA) inhibited the global DNA methylation, and some causal genes (e. g., GhDMT13, GhDAMT2, GhALKBH12, GhDM7) were also identified. Conclusions In this study, all the findings indicated the interplay between histone acetylation and DNA methylation, supporting their important roles and providing precious clues for the epigenetic modifications associated with DNA methylation in the fiber development of cotton.