In situ genome sequencing of early mouse embryos

Understanding the functional impact of genome organization requires integration of the one dimensional DNA sequence and the 3-D spatial context in single cells. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific developmental transitions in embryonic genome organization, revealed the existence of large heterogeneous chromatin domains in single zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how in situ genome sequencing can directly connect structure and function across length scales from single base pairs to whole organisms.