Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. 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 changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

理解基因组组织需要整合 DNA 序列和三维空间背景；然而，现有的全基因组方法缺乏碱基对序列分辨率或直接空间定位。在这里，我们描述了原位基因组测序 (IGS)，这是一种在完整生物样本中同时对基因组进行测序和成像的方法。我们将 IGS 应用于人类成纤维细胞和早期小鼠胚胎，在空间上定位单个细胞核中的数千个基因组位点。使用这些数据，我们表征了整个胚胎阶段基因组结构中亲本特异性的变化，揭示了受精卵中的单细胞染色质域，并揭示了个体胚胎内全局染色体定位的表观遗传记忆。