H3K27me3 dictates atypical genome-nuclear lamina interactions and allelic asymmetry during early embryogenesis

Abstract

The very first days of mammalian embryonic development are accompanied by epigenetic reprogramming and extensive changes in nuclear organization. In particular, genomic regions located at the periphery of the nucleus, termed lamina-associated domains (LADs), undergo major rearrangements after fertilization. However, the role of LADs in regulating gene expression as well as the interplay with various chromatin marks during preimplantation development remains elusive. In this study, we obtained single-cell LAD profiles coupled with the corresponding gene expression readout throughout the first days of mouse development. We detect extensive cell-cell LAD variability at the 2-cell stage, which surprisingly does not seem to functionally affect gene expression. This suggests an unusual uncoupling between 3D-nuclear genome organization and gene expression during totipotent developmental stages. By analyzing LAD dynamics and chromatin states across early developmental stages in an allelic-specific manner, we identify genomic regions that transiently detach from the nuclear lamina and are enriched by non-canonical H3K27me3. Upon maternal knock-out of a component of the Polycomb repressive complex 2 and concomitant loss of H3K27me3 during early embryogenesis, these regions relocate to the lamina at the 2-cell stage. Our results suggest that H3K27me3 is the prime determinant in establishing the atypical distribution of the genome at the nuclear periphery during the first days of embryonic development. This study provides insight into the molecular mechanisms regulating nuclear organization of parental genomes during very early mammalian development.

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

“…The observation that precisely those Xi regions that lose genome-lamina interactions strongly accumulate H3K27me3, suggests a potentially antagonistic effect between lamina association and polycomb-deposited H3K27me3 during XCI. A similar phenomenon has recently been described in two unrelated systems, namely K562 cells and preimplantation embryos, where removal of H3K27me3 led to increased genome-lamina interactions (Guerreiro et al, 2023;Siegenfeld et al, 2022). Importantly, our multifactorial analysis implies that the loss of genome-lamina interactions starts just prior to accumulation of H3K27me3.…”

“…With Dam&ChIC, we aimed to map the interactions of the Xi with the nuclear lamina and dissect the interplay with hPTMs H3K27me3 and H3K9me3. To this end, we induced random XCI in vitro , by differentiating our two previously derived female hybrid (CAST/Eij x 129/Sv) embryonic stem cell (ESC) lines expressing Dam-LMNB1 and Dam-scFv-H3K27me3 (Guerreiro et al, 2023; Rang et al, 2022) (Fig. 4a).…”

“…These mESC lines are derived from female cells and do not contain a Y chromosome. The Dam-LMNB1 or Dam-scFv-H3K27me3 constructs were previously integrated in these cells using CRISPR targeting (Guerreiro et al, 2023; Rang et al, 2022). Both ESC lines express the Dam-POI under the control of the AID degron system.…”