3D Genome Organization During Meiosis And Development Of Multi-omics Genomics Technologies

In the past two decades,many new methods were developed and used to exploring the higher order chromatin organization in different species and different biological processes.These studies deepened our understanding about the mechanism and function of higher order chromatin organization,which also promoted the research progress in other fields,such as transcription regulation,development and diseaseTetrahymena thermophila has two nuclei in the same cell,which both developed from the same zygotic nucleus during conjugation but finally differ in both function and genome structures.Here,we explored the higher order chromatin organization of the two distinct nuclei in Tetrahymena thermophila with Hi-C and HiChIP.Our results showed there are crescent-specific chromosome interactions in the micronucleus(MIC)when the MIC elongated and enter meiosis.All telomeres and centromeres in the crescent MIC were clustering together,respectively.We found there are no A/B compartments,topologically associating domains(TAD)and regulatory chromatin loops in the macronucleus(MAC)of Tetrahymena thermophila,while there are chromosome territories.There are also no A/B compartments and TADs in the MIC,but we found there are TAD-like structures in the MIC of Tetrahymena thermophila.The boundaries of the TAD-like structures are consistent with the chromosome breakage sequences(CBSs)on the MIC genome,and each of the TAD-like structures in the MIC were correspond to a chromosome in the MAC.In summary,our work provided an overview of the higher order chromatin organization in the two distinct nuclei of Tetrahymena thermophila and suggested that the TAD-like structures in the MIC may related to the formation of the MAC chromosomes during conjugation.Mouse spermatogenesis is a complex process which contains cell differentiation,meiosis and spermiogenesis.Here,we combined Hi-C,ATAC-seq and ChIP-seq to study the higher order chromatin organization,chromatin accessibility and related chromatin binding proteins during mouse spermatogenesis.We found the higher order chromatin structures were reorganized during mouse spermatogenesis.The A/B compartments were continuously retained but the strength of A/B compartments was changed during spermatogenesis,which reach its lowest at pachytene during meiosis.TADs and chromatin loops also reorganized during spermatogenesis which almost lost at pachytene stage.And the disappearing of the TADs or chromatin loops at pachytene was independent with the changes of chromatin accessibility,transcriptional activity or the chromatin binding of CTCF/cohesin.In addition,we found the reestablished chromatin loops in the transcriptional inert sperm were associated with genes expressed during early embryonic development,which suggesting that higher order chromatin structures may have epigenetic functions.In addition to exploring the higher order chromatin organization in Tetrahymena thermophila and during mouse spermatogenesis with existing methods.We initially established a new method called HiATAC to capture the open chromatin interactions which is useful to study enhancer promoter interactions.We also initially established a new method named single-cell AR which could exploring gene expression and chromatin accessibility together at single-cell level.