Organ development is orchestrated by cell- and time-specific gene regulatory networks. In this study, we investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood. By acquiring snATAC-seq (single-nucleus assay for transposase accessible chromatin using sequencing) profiles for ~90,000 cells spanning 11 stages, we mapped cerebellar cell types and identified candidate cis-regulatory elements (CREs). We detected extensive spatiotemporal heterogeneity among progenitor cells and a gradual divergence in the regulatory programs of cerebellar neurons during differentiation. Comparisons to vertebrate genomes and snATAC-seq profiles for ∼20,000 cerebellar cells from the marsupial opossum revealed a shared decrease in CRE conservation during development and differentiation as well as differences in constraint between cell types. Our work delineates the developmental and evolutionary dynamics of gene regulation in cerebellar cells and provides insights into mammalian organ development.

器官发育是由细胞和时间特异性基因调控网络协调的。在这项研究中，我们调查了小鼠小脑从早期神经发生到成年期发育的调控基础。通过获取跨越 11 个阶段的约 90,000 个细胞的 snATAC-seq（使用测序的转座酶可及染色质的单核测定）谱，我们绘制了小脑细胞类型并确定了候选顺式-监管要素（CRE）。我们检测到祖细胞之间广泛的时空异质性和分化过程中小脑神经元调节程序的逐渐分歧。与来自有袋负鼠的约 20,000 个小脑细胞的脊椎动物基因组和 snATAC-seq 谱的比较揭示了在发育和分化过程中 CRE 保护的共同减少以及细胞类型之间的约束差异。我们的工作描述了小脑细胞基因调控的发育和进化动力学，并为哺乳动物器官发育提供了见解。