News Release

Salk teams advance efforts to treat, prevent and cure brain disorders, via NIH brain atlas

New papers describe the diversity of neurons in the mouse brain and establish tools for studying the human brain

Peer-Reviewed Publication

Salk Institute

Science Illustration

image: A representation of cell diversity in the brain. Individual nuclei are colored in the bright hues of t-SNE plots used in epigenomics analysis to distinguish individual brain cell types. Layers of background color suggest extrinsic factors that influence cell function. view more 

Credit: Michael Nunn, Salk Institute

LA JOLLA—(October 6, 2021) It takes billions of cells to make a human brain, and scientists have long struggled to map this complex network of neurons. Now, dozens of research teams around the country, led in part by Salk scientists, have made inroads into creating an atlas of the mouse brain as a first step toward a human brain atlas.

The researchers, collaborating as part of the National Institute of Health’s BRAIN Initiative Cell Census Network (BICCN), report the new data today in a special issue of the journal Nature. The results describe how different cell types are organized and connected throughout the mouse brain.

“Our first goal is to use the mouse brain as a model to really understand the diversity of cells in the brain and how they’re regulated,” says Salk Professor and Howard Hughes Medical Institute Investigator Joseph Ecker, co-director of the BICCN. “Once we’ve established tools to do this, we can move to working on primate and human brains.”

The NIH Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative is “a large-scale effort that seeks to deepen understanding of the inner workings of the human mind and to improve how we treat, prevent and cure disorders of the brain.” Since its initial funding in 2014, the BRAIN Initiative has awarded more than $1.8 billion in research awards.

The BICCN, one subset of the BRAIN Initiative, specifically focuses on creating brain atlases that describe the full plethora of cells—as characterized by many different techniques—in mammalian brains. Salk is one of three institutions that were given U19 awards to act as central players in generating data for the BICCN.

“This is not just a phone book for the brain,” says Margarita Behrens, a Salk associate research professor who helped lead the new BICCN papers. “In the long run, to treat brain diseases, we need to be able to hone in on exactly which cell types are having trouble.”

The special issue of Nature has 17 total BICCN articles, including five co-authored by Salk researchers that describe approaches to studying brain cells and new characterizations of subtypes of brain cells in mice. Some highlights include:

  • DNA Methylation Analysis

While other papers in the special issue relate to the function or structure of mouse brain cells, the work led by Ecker, Behrens and their colleagues largely focuses on the epigenomics of brain cells in mice. Every cell in a mouse brain contains the same sequence of DNA, but variations in how this DNA is regulated—its so-called “epigenome”—give cells their unique identity. The arrangement of methyl chemical groups on the cytosine base in DNA (known as “cytosine methylation”), which specifies when genes are to be turned on or off, are one form of epigenomic regulation that may highly influence disease and health in the brain.

In one of the new papers, the Salk team analyzed 103,982 mouse brain cells using single-cell DNA methylation sequencing. This approach, developed in the Ecker lab, lets researchers study the pattern of methyl chemical groups on each strand of DNA in brain cells.

When they applied the technique to the thousands of cells collected from 45 different regions of the mouse brain, they were able to identify 161 clusters of cell types, each distinguished by their pattern of methylation.

“Before now, there have been a handful of ways to describe brain cells based on their location or their electrical activity,” says Hanqing Liu, a graduate student in the Ecker lab and co-first author of the paper. “We’ve really extended the definition of cell type here and used epigenomics to define hundreds of potential cell types.”

The team went on to show that the methylation patterns could be used to predict where in the brain any given cell came from—not just within broad regions but down to specific layers of cells within a region. This means that eventually, drugs could be developed that act only on small groups of cells, by targeting their unique epigenomics.

  • Neuron Destination Patterns

In another paper, co-authored by Ecker and Salk Professor Edward Callaway, researchers studied the association between DNA methylation and neural connections. The team developed a new way of isolating cells that connect regions of the brain, then studying their methylation. They used the approach on 11,827 individual mouse neurons, all extending outward from the mouse cortex. The patterns of methylation in the cells, they discovered, correlated with cells’ projection (destination) patterns. Neurons that led from the motor cortex to the striatum, for instance, had distinct epigenomics from neurons that connected the primary visual cortex and the thalamus.

“Neurons don’t function in isolation, they function by communicating with each other, so understanding how these connections are established and how they work is really fundamental to understanding the brain,” says Zhuzhu Zhang, a Salk postdoctoral fellow and a co-first author of the paper with graduate student Jingtian Zhou, both members of Ecker’s laboratory.

The researchers say that the new data on the mouse brain cells is merely the first step in creating a complete atlas of the mouse brain—let alone the human brain. But understanding what differentiates cell types is critical to future research and future brain therapeutics.

“In these foundational studies, we’re describing the ‘parts list’ for the brain,” says Callaway. “Having this parts list is revolutionary, and will open up a whole new set of opportunities for studying the brain.”


Hanqing Liu and Jingtian Zhou, both of Salk, were co-first authors on the DNA methylation atlas paper; Zhuzhu Zhang and Jingtian Zhou, also both of Salk, were co-first authors on the cortical projection paper. The methylation atlas work was supported by the National Institutes of Mental Health (U19MH11483), the National Human Genome Research Institute (R01HG010634) and the Howard Hughes Medical Institute. The cortical projection paper was supported by the National Institute of Mental Health (U19MH114831and R01MH063912), the National Eye Institute (R01EY022577 and F31 EY028853) and the Howard Hughes Medical Institute.

For More Information:


Title: DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution



Title: Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain



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


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