The sequencing data used in "Dynamic changes in 3D chromatin structure during the two rounds of mitosis in plant male gametogenesis"

Chromatin higher-order structure plays an important role in genome stability maintenance and gene transcriptional regulation; however, the dynamics of the three-dimensional (3D) organization of the genome in male gametophytes during the two rounds of mitosis remains elusive. Here, we used the optimized single-nucleus high-throughput chromosome conformation capture (Hi-C) method (termed agarose-C) in combination with low-input Hi-C to investigate changes in 3D chromatin structure in four types of male gametophytes. The reconstructed genome structures show that microspore nuclei develop in two different directions. On one hand, although the 3D chromatin organization in generative nuclei is similar to that in microspore nuclei, vegetative nuclei lose chromosomal territories and display dispersed centromeres and refined A/B compartments and Topologically Associating Domains (TADs). On the other hand, sperm nuclei have the most compact chromatin structure, switched A/B compartments, and refined TADs. Moreover, we found that H2B.8 is involved in chromatin compaction in sperm nuclei by preventing interchromosomal interactions. Our data suggest that the special structures of vegetative and sperm nuclei facilitate cell type-specific expression patterns.