BACKGROUND: Chromatin higher-order structure plays an important role in genome stability maintenance and gene transcriptional regulation
however, the dynamics of the three-dimensional (3D) chromatin in male gametophytes during the two rounds of mitosis remains elusive. RESULTS: Here, we use the optimized single-nucleus and low-input Hi-C methods to investigate changes in 3D chromatin structure in four types of male gametophyte nucleus at different stages. The reconstructed genome structures show that microspore nuclei develop towards two different directions. Although the 3D chromatin organization in generative nuclei is similar to that in microspore nuclei, vegetative nuclei lose chromosome territories, display dispersed centromeres, and switched A/B compartments, which are associated with vegetative specific gene expression. Additionally, we find that there is an active transcriptional center in sperm nuclei, emphasizing the transcription in Arabidopsis sperm is not completely inhibited despite the chromosomes being condensed. CONCLUSIONS: Our data suggest that the special 3D structures of vegetative and sperm nuclei contribute to cell type-specific expression patterns.