Single-Cell Atlas Captures Two Key Epigenetic Layers in Human Cells
For the first time, scientists have mapped DNA methylation and chromatin contacts together in thousands of human cells.
Epigenetics governs which of a cell’s genes are active and which remain silent, enabling the same 3 billion letters of DNA to be used for entirely different cell types and functions.
Researchers at the Salk Institute have recently developed the first body-wide single-cell atlas that simultaneously captures two major epigenetic systems—DNA methylation and 3D genome folding.
Features of the epigenome
The epigenome—the chemical modifications and chromatin-based organization of the genome—modulates gene transcription, enabling cell type-specific activity.
There are multiple layers of epigenetic regulation, including histone modification, direct chemical additions to DNA, and 3D genome folding.
“Methylation places small chemical tags on DNA bases; in the right places, those tags can silence a gene or mark regulatory elements, so the methylation pattern is tightly linked to a cell's identity,” Dr. Joseph Ecker, a professor at the Salk Institute and a co-corresponding author of the new work, told Technology Networks.
“3D folding brings distant stretches of DNA together through loops, domains, and compartments, so regulatory elements like enhancers can physically reach the genes they control,” Ecker explained. “In short, methylation marks which elements are usable, and the 3D structure determines which of those elements actually reach which genes.”
Epigenetic modifications can arise from environmental factors, connecting our environment, diet, and lifestyle to gene expression and cellular function.
Understanding how the genome is organized and how epigenetic modifiers control gene expression is also key to understanding how genetic variants impact disease.
Measuring two layers of epigenetic control
How DNA methylation and 3D genome architecture vary across distinct cell types has been largely understudied. Previous efforts to map DNA methylation and 3D genome structures used bulk tissue samples, which can obscure cell type-specific signals.
Ecker and his colleagues used single-nucleus methyl-3C sequencing to simultaneously measure 3D chromatin contacts and DNA methylation in a single nucleus.
“Measuring both layers in the same single cell lets us ask whether they agree, rather than assume they do,” said Ecker. “Because both readouts came from the same nucleus, we could directly compare what each one says about a cell's state and catch the cases where they disagree.”
The researchers profiled over 86,000 single nuclei from 16 human tissues, revealing 35 major cell types and 206 subtypes based on their epigenetic signature.
“This combined, cell-type-resolved view is also what makes the atlas valuable as labeled training data for models that predict how genetic variants act,” said Ecker.
Epigenetic regulation is highly cell-type specific
In building the atlas, the researchers discovered the scale of cell-type-specific epigenetic regulation, finding “more than 1.36 million differentially methylated regions and over 283,000 differential chromatin loops across the body,” Ecker explained.
Different cell lineages had distinctive signatures of DNA methylation and 3D genome organization, and in some cells, the two layers of epigenetic regulation appeared to tell different stories about cell state.
“In skeletal muscle we found fibers that look like mature muscle by their 3D folding but still carry the methylation signature of muscle stem cells, and the reverse almost never happens,” noted Ecker. “We saw similar mismatches in Schwann cells and placental trophoblasts, which suggests that different epigenetic features update on different time scales.”
The team suggests that where DNA methylation and 3D genome architecture mismatch, the cell may have been caught mid-differentiation, providing insight into how cells shift state. Based on the examples of mismatching identified in the atlas, it appears that 3D genomic architecture “updates” to the new cell state first, with methylation changes following behind.
Epigenetic mismatch may therefore flag cells that are switching state, which could be important for understanding disease processes and progression.
Understanding the impact of epigenetics on disease
Most disease-causing genetic variants are found in the regions of the genome that don’t encode proteins, making it difficult to identify how they contribute to disease.
Uncovering Hidden Genetic Causes of Sudden Cardiac Death With Long-Read Sequencing
It explores how long-read sequencing was used to identify a pathogenic dystrophia myotonica protein kinase (DMPK) repeat expansion associated with inherited cardiac disease and sudden cardiac death after previous testing failed to find a diagnosis.View Webinar
“When we overlaid known risk variants onto the atlas, clear pairings emerged: blood-glucose variants in endocrine cells, atrial fibrillation variants in heart muscle, balding variants in skin fibroblasts, and bipolar disorder and schizophrenia variants in neurons,” explained Ecker. “Adding the 3D genome layer helps connect a non-coding variant to the gene it physically contacts in a specific cell type.”
“Because different cell types are organized differently, some are more vulnerable than others to a given disease-risk genetic variant.” — Prof. Joseph Ecker.
In a companion paper, researchers led by Dr. Bing Ren at the New York Genome Center used data from the atlas to illustrate how microglia—the brain’s immune cells—change with age.
They found that between ages 50 and 75, microglia established during embryonic development were replaced by cells whose epigenetic signatures resembled those of immune cells from the blood. The replacement microglia-like cells had elevated inflammatory signatures, indicating that they may contribute to neuroinflammation in the aging brain.
Non-CG methylation plays a broader role in epigenetic regulation
One of the most surprising findings of the new study surrounded non-CG methylation.
Usually, DNA is methylated at a cytosine nucleotide followed by a guanine nucleotide. In non-CG methylation, a methyl group is added to a cytosine base that is not part of a cytosine-guanine sequence.
Non-CG methylation was previously thought to only exist in neurons, glia, and stem cells, and its biological role remains unclear.
“[A stand-out finding from the atlas was] how much cell-identity information is carried by non-CG methylation in tissues where we didn't expect it, including muscle, pancreas, and immune cells, rather than only brain and stem cells,” noted Ecker.
Neutrophil Biology and Defense Against Pathogens
This poster explores the role of neutrophils as the first line of defense against invading microorganisms.View Poster
While the levels of non-CG methylation detected in other tissues were lower than in brain and stem cells, the non-CG methylation patterns carried information on cell identity.
“Rather than a quirk of a few cell types, it looks like a broader, if subtler, part of the regulatory landscape than the field had assumed,” explained Ecker.
An open-access resource
The atlas is freely available online and helps researchers to visualize DNA methylation and genome architecture across the tissues, cell types, and subtypes analyzed in the study.
The data from the atlas can be used to train AI algorithms that predict the functional impact of genetic variants on disease, thereby increasing predictive accuracy.
The atlas, developed as part of the National Institutes of Health 4D Nucleome Program, also forms a reference point for future time-course studies.
“The clear next step is the fourth dimension: time,” said Ecker. “This atlas is a snapshot, and we want to understand how genome structure and methylation change as cells develop, age, and respond to disease.”
Reference: Zhou J, Wu Y, Liu H, et al. Human body single-cell atlas of three-dimensional genome organization and DNA methylation. Science. 2026;393(6809):eadx0673. doi: 10.1126/science.adx0673
About the interviewee:
Dr. Joseph Ecker is a professor in the Plant Molecular and Cellular Biology Laboratory at the Salk Institute and is the director of the Genomic Analysis Laboratory. He also holds the Salk International Council Chair in genetics and is a Howard Hughes Medical Institute investigator.
His current research focuses on genomic and epigenomic regulation in plants and mammals and the application of DNA sequencing technologies for genome-wide analysis of DNA methylation, transcription, and gene function.
Add Technology Networks as a preferred Google source to see more of our trusted coverage.
