An atlas of gene regulatory elements in adult mouse cerebrum.
IF: 69.504
Cited by: 69


The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.


Spatial Transcriptomics

MeSH terms

Atlases as Topic
Chromatin Assembly and Disassembly
Gene Expression Regulation
Genetic Predisposition to Disease
Mice, Inbred C57BL
Nervous System Diseases
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA
Single-Cell Analysis


Li, Yang Eric
Preissl, Sebastian
Hou, Xiaomeng
Zhang, Ziyang
Zhang, Kai
Qiu, Yunjiang
Poirion, Olivier B
Li, Bin
Chiou, Joshua
Liu, Hanqing
Pinto-Duarte, Antonio
Kubo, Naoki
Yang, Xiaoyu
Fang, Rongxin
Wang, Xinxin
Han, Jee Yun
Lucero, Jacinta
Yan, Yiming
Miller, Michael
Kuan, Samantha
Gorkin, David
Gaulton, Kyle J
Shen, Yin
Nunn, Michael
Mukamel, Eran A
Behrens, M Margarita
Ecker, Joseph R
Ren, Bing

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