Tracing epigenetic changes in early human embryogenesis

Abstract

Epigenetic alterations are essential for human embryonic development, regulating gene expression and determining cell fate. However, understanding these processes in human embryonic cells has been challenging due to ethical constraints and technical limitations. Here, we analyzed 400 single-cell-derived colonic clones from 15 individuals using whole-genome sequencing (WGS), whole-genome methylation sequencing (WGMS), and transcriptome sequencing to trace epigenetic dynamics during early development. Using somatic mutations as barcodes, I constructed phylogenetic trees of embryonic lineages and integrated DNA methylation data to identify early embryonic epimutations (EEEs). On average, 2,100 EEE regions per donor were identified, defined as regions with at least six consecutive CpG sites showing methylation changes. A total of 12,650 unique EEE regions were characterized, with a strong enrichment in promoter regions and recurrent patterns across donors, highlighting their conserved regulatory roles. Somatic mutations as molecular clocks revealed that many methylation changes were fixed prior to gastrulation and stably inherited across subsequent cell generations. Integration with transcriptomic data confirmed functional correlations between promoter methylation and gene expression. Additionally, I quantified methylation changes by categorizing them into technical errors, early embryonic changes, and age-dependent changes, providing a novel framework for understanding their distinct contributions to the overall methylation landscape. I estimated that early embryogenesis involves ~700,000 methylation changes, while aging results in ~10,000 changes per year. EEE regions correspond to a subset of early embryonic methylation changes, comprising approximately 40,000 CpG changes at the single-CpG resolution. In summary, this study provides the first genome-wide, base-resolution insights into early epigenetic mosaicism and age-associated methylation dynamics in humans, made possible through the integration of multi-omics technologies at the single-cell level. This study holds significance as the first to quantitatively analyze methylation changes at the single CpG level within a specific cell type across the human lifespan. These findings enhance our understanding of the regulatory mechanisms shaping early development and aging.