DNA methylation atlas of the mouse brain at single-cell resolution

Abstract

Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing1,2 to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data3 enabled prediction of high-confidence enhancer–gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments4. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.

Comparative cellular analysis of motor cortex in human, marmoset and mouse

“…To further characterize the epigenomic landscape of M1 cell types, we profiled DNAm from humans, marmosets and mice 29 using snmC-seq2 (ref. 30 ) (Extended Data Fig.…”

“…28 Department of Physiology and Biophysics, Washington National Primate Research Center, University of Washington, Seattle, WA, USA. 29…”

A multimodal cell census and atlas of the mammalian primary motor cortex

“…5). Similarly, we identified transcription factors showing cell-type specificity supported by both RNA expression and DNA-binding motif enrichment in cell subclasses 37,39 (Methods) (Extended Data Fig. 7).…”

“…We describe a synthesis of eleven companion studies through a coordinated multi-laboratory effort. In these studies, we derive a cross-species consensus molecular taxonomy of cell types using scRNA-seq or single-nucleus RNA sequencing (snRNA-seq), DNA methylation and chromatin accessibility data [37][38][39][40] . In mouse, we map the spatial cellular organization by multiplexed error-robust fluorescence in situ hybridization (MERFISH) 41 , characterize morphological and electrophysiological properties by multimodal profiling using patch clamp recording, biocytin staining and scRNA-seq (Patch-seq) 42,43 , describe the cellular input-output wiring diagrams by anterograde and retrograde tracing 44 , identify glutamatergic neuron axon projection patterns by Epi-retro-seq 45 , Retro-MERFISH 41 and single-neuron complete morphology reconstruction 46 , and describe transgenic driver lines targeting glutamatergic cell types on the basis of marker genes and lineages 47 .…”

Cortical Cartography: Mapping Arealization Using Single-Cell Omics Technology

“…Single-cell transposome hypersensitive site sequencing can generate maps of TFs, regulatory elements, and DNA accessibility to characterize extensive cellular diversity in the human cortex and cerebellum (Lake et al, 2018). Single-cell DNA methylation analysis has been shown to identify excitatory and inhibitory neuron subtypes (Luo et al, 2017), and singlenucleus methylation assays have led to the construction of taxonomies defined by signature genes, regulatory elements and TFs in 45 regions of the mouse cortex, hippocampus, striatum, palladium, and olfactory areas (Liu et al, 2021). This comprehensive assessment of the mouse brain cell epigenome elucidates the regulatory landscape that supports cell fate specification, while also revealing repetitive use of these regulators found in excitatory versus inhibitory neurons to further distinguish subtypes.…”