Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
Nature. 2023 Dec;624(7991):366-377. doi: 10.1038/s41586-023-06805-y. Epub 2023 Dec 13.
Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq) technologies to generate 301,626 methylomes and 176,003 chromatin conformation-methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 cross-modality-annotated subclasses. We identified 2.6 million differentially methylated regions across the genome that represent potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide spatial transcriptomics data validated the association of spatial epigenetic diversity with transcription and improved the anatomical mapping of our epigenetic datasets. Furthermore, chromatin conformation diversities occurred in important neuronal genes and were highly associated with DNA methylation and transcription changes. Brain-wide cell-type comparisons enabled the construction of regulatory networks that incorporate transcription factors, regulatory elements and their potential downstream gene targets. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a whole-brain SMART-seq dataset. Our study establishes a brain-wide, single-cell DNA methylome and 3D multi-omic atlas and provides a valuable resource for comprehending the cellular-spatial and regulatory genome diversity of the mouse brain.
胞嘧啶 DNA 甲基化在大脑发育中至关重要，并与各种神经紊乱有关。在空间背景下了解整个大脑中的 DNA 甲基化多样性，对于构建完整的大脑细胞类型及其基因调控景观的分子图谱至关重要。在这里，我们使用单核 DNA 甲基组测序 (snmC-seq3) 和多组学测序 (snm3C-seq) 技术，从成年小鼠大脑的 117 个解剖区域生成了 301,626 个甲基组和 176,003 个染色质构象-甲基组联合图谱。通过迭代聚类，并与全脑转录组和染色质可及性数据集相结合，我们构建了一个基于甲基化的细胞分类学，包含 4,673 个细胞群和 274 个跨模态注释子类。我们在整个基因组中鉴定了 260 万个差异甲基化区域，它们代表潜在的基因调控元件。值得注意的是，我们观察到在细胞类型内和跨脑区的基因和调控元件上存在空间胞嘧啶甲基化模式。全脑空间转录组学数据验证了空间表观遗传多样性与转录的关联，并提高了我们表观遗传数据集的解剖映射。此外，染色质构象多样性发生在重要的神经元基因中，与 DNA 甲基化和转录变化高度相关。全脑细胞类型比较使构建包含转录因子、调控元件及其潜在下游基因靶标的调控网络成为可能。最后，基因内 DNA 甲基化和染色质构象模式预测了在全脑 SMART-seq 数据集中观察到的替代基因亚型表达。我们的研究建立了一个全脑单细胞 DNA 甲基化组和 3D 多组学图谱，并为理解小鼠大脑的细胞-空间和调控基因组多样性提供了有价值的资源。
