Single-cell multi-omics sequencing revealed cytoskeleton defects led to human embryonic arrest characterized with zygotic genome activation

Human in vitro-fertilized (IVF) embryos exhibit low developmental capabilities. However, the mechanisms underlying human embryonic arrest remain unclear. Here, using single-cell multi-omics sequencing approach, we simultaneously dissected the alteration of transcriptome, chromatin accessibility and DNA methylome in human early embryos arrested for unexplained reasons. Human arrested embryos displayed transcriptome disorders, including distorted microtubule cytoskeleton, increased genomic instability and impaired glycolysis, which were coordinated with multiple epigenetic reprogramming defects. Moreover, we identified Aurora A kinase (AURKA) repression was a reason for human embryonic arrest. Mechanistically, human arrested embryos from AURKA inhibited group resembled the reprogramming abnormalties of clinically arrested embryos in terms of transcriptome, DNA methylome, chromatin accessibility and H3K4me3. Through mitosis-independent sequential activation of zygotic genome in human arrested embryos, we found YY1 contributed to human major zygotic genome activation (ZGA). Collectively, our study decodes the reprogramming abnormalities and mechanisms for human embryonic arrest and key regulators of human ZGA. We collected human arrested zygote, 2-cell, 4-cell and 8-cell embryos that were with no further development for another two days, followed by performing single-cell multi-omics sequencing including transcriptome, DNA methylome and chromatin accessibility. Additionally, we performed single-embryo multi-omics sequencing of human 8-cell embryos (3PN) from YY1 knockdown group and control group, single-embryo RNA sequencing of human 8-cell embryos (3PN) from KDOAM25 treated group and control group, single-cell multi-omics sequencing of human arrested zygote (3PN) from AURKA inhibited group and control zygotes, and single-cell RNA sequencing of mouse arrested zygote from AURKA inhibited group and control embryos (raw sequencing data of mouse embryos have been deposited in Genome Sequence Archive (GSA) database with the accession number CRA012505; processed data for mouse samples are available in the OMIX database (China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences) with accession number OMIX004867). *************************************************************** Due to the relevant regulation from China's Ministry of Science and Technology related to the export of genetic information and materials, all raw sequencing data of human embryos reported in this study have been deposited in Genome Sequence Archive (GSA) for human database with the accession number HRA003366. ***************************************************************