Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos

Mo Chen,Shaorong Gao,Qianshu Zhu,Lei Yang,Hong Wang,Yanhe Li,Cizhong Jiang,Xiaoyu Liu,Yanhong Zhao,Chong Li,Liang Gu,Xiaochen Kou,Lingyue Yang,Ruimin Xu

doi:10.1038/s41467-020-15607-z

Abstract

The oocyte cytoplasm can reprogram the 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 examine higher order chromatin structures of mouse SCNT embryos using a low-input Hi-C method. We find that donor cell chromatin transforms to the metaphase state rapidly after SCNT along with the dissolution of typical 3D chromatin structure. Intriguingly, the genome undergoes a mitotic metaphase-like to meiosis metaphase II-like transition following activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerge following metaphase exit. TADs are further removed until the 2-cell stage before being progressively reestablished. Obvious defects including stronger TAD boundaries, aberrant super-enhancer and promoter interactions are found in SCNT embryos. These defects are partially caused by inherited H3K9me3, and can be rescued by Kdm4d overexpression. These observations provide insight into chromatin architecture reorganization during SCNT embryo development.

Highlights

The oocyte cytoplasm can reprogram the somatic cell nucleus into a totipotent state, but with low efficiency
To reveal the establishment of higher order chromatin structure during the early development of somatic cell nuclear transfer (SCNT) embryos, we optimized a small-scale in situ Hi-C method based on a recent study[17]
We collected mouse cumulus cells (CCs), which were used as donor cells for SCNT, and reconstructed embryos at different stages, including the 0.5 h post-injection (0.5-hpi), 1-hpi, 1 h postactivation (1-hpa), 6-hpa, 12-hpa, early-2-cell embryo, late-2-cell embryo, 4-cell embryo, 8-cell embryo, morula embryo, as well as inner cell mass (ICM) and trophectoderm (TE) from blastocyst stage embryos and performed Hi-C experiments at each stage (Fig. 1a, Supplementary Table 1)

Summary

Introduction

The oocyte cytoplasm can reprogram the somatic cell nucleus into a totipotent state, but with low efficiency. We examine higher order chromatin structures of mouse SCNT embryos using a low-input Hi-C method. Obvious defects including stronger TAD boundaries, aberrant super-enhancer and promoter interactions are found in SCNT embryos These defects are partially caused by inherited H3K9me[3], and can be rescued by Kdm4d overexpression. In Drosophila embryos, higher order chromatin structure emerges during zygotic genome activation (ZGA) and TAD boundary formation is transcription independent[19]. We examine the 3D chromatin structure across consecutive stages of SCNT embryo development and find that higher order chromatin architectures, including compartments and TADs, are dissolved and reestablished in a stage-specific and coordinated manner during SCNT embryogenesis. Our findings provide a high-resolution map of how the mature 3D chromatin structure of somatic cells is reprogrammed to a totipotent state after transplanting into enucleated oocytes

Methods

Results

Conclusion