Chromatin architecture reorganization in somatic cell nuclear transfer embryos

The oocyte cytoplasm can reprogram somatic cell nucleus into a totipotent state but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examined higher-order chromatin structures of mouse SCNT embryos using an optimized low-input Hi-C approach. We found that the donor cell chromatin transformed to metaphase state rapidly after injection along with the dissolution of typical 3D chromatin structures. Intriguingly, the donor cell genome underwent a transition from mitotic metaphase-like state to meiosis metaphase II-like state within one hour after activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerged at 6 hours after activation. Then TADs were gradually removed until the 2-cell stage and then progressively reestablished. We found that relative few distal (> 2 Mb) interactions were present in 2-cell stage SCNT embryos. Also, obvious differences in compartment and TAD organization between fertilization-derived and SCNT embryos were observed in early stages (2-8 cell stages). Many interactions between super-enhancers and promoters were not successfully established in SCNT embryos, and these interactions were further shown important for zygotic genome activation (ZGA). Moreover, we demonstrate that the aberrant chromatin architecture reorganization in SCNT embryos may be due to the persistent H3K9me3 and can be partially rescued by the Kdm4d overexpression. This study therefore provides novel insight into chromatin architecture reorganization during SCNT embryo development. 1. Examination of chromatin architecture organization in 13 SCNT embryo development time point including cumulus cell (CC), 0.5-hpi, 1-hpi, 1-hpa, 6-hpa, 12-hpa, early-2-cell, late-2-cell, 4-cell, 8-cell, morula, inner cell mass (ICM) and trophectodern (TE). 2. Examination of chromatin architecture organization in early-2-cell embryos of overexpression Kdm4d and TSA treatment. 3. Eamination of chromatin architecture organization in mouse R1 ESCs. 4. Eamination of histone 3 lysine 9 tri-methylation in CC. 5. RNA-seq data for ICM and TE.