This work shows that TAD-scale lamina-release primes developmental loci days before transcription, revealing nuclear lamina reorganization as an active, instructive driver of cell-fate decisions rather than a passive consequence of gene activation.
Genome-lamina interactions undergo extensive reconfiguration during organogenesis rather than gastrulation, with lamina-release at developmental gene regulatory domains occurring in multipotent progenitors prior to transcriptional activation, thereby priming loci for future cell-fate decisions through a mechanism that coordinates with transcription factor binding and is spatially constrained by TAD boundaries.
Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell- fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis. We find that genome-lamina interactions remain relatively uniform between germ layers following gastrulation but are extensively reconfigured in diverse tissues during later organogenesis. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released in early multipotent progenitors at key developmental genes and their surrounding regulatory domains. This “lamina-release” often precedes gene expression at later developmental stages, suggesting it primes regulatory domains for future potential activation. Conversely, lamina-release coincides with chromatin opening at sites of crucial limb transcription factor binding, and so is closely intertwined with the regulatory machinery driving limb formation. Finally, we show that the boundaries of topologically-associated domains (TADs) constrain the spread of lamina-release at a limb gene locus. This ensures independent lamina dynamics between neighbouring domains. Together, our data suggest a previously unrecognised process where genome-lamina interactions are selectively released at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insights into cell-fate decisions in vivo.