There is an explosion of single-cell genomics profiling technologies. Although major advances have been made in measuring gene expression and DNA accessibility, assays specific to epigenetic modifications have been limited. Now, researchers have developed a technique that makes it possible to examine how different versions of histones bind to the genome in tens of thousands of individual cells at the same time. To do this, they combined CUT&Tag technology with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. The technique was applied to the mouse brain and can be used to study epigenetics at a single-cell level in other complex tissues.

The study is published in Nature Biotechnology, in the paper, “Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.”

“This technique will be an important tool for examining what makes cells different from each other at the epigenetic level,” said Marek Bartosovic, PhD, postdoctoral fellow at the department of medical biochemistry and biophysics, Karolinska Institute. “We anticipate that it will be widely implemented by the broad biomedical community in a wide variety of research fields.”

Epigenetics play a crucial role in the interpretation of genetic information and allows the cells to execute specialized functions. Until recently, it was not possible to look at histone modifications of an individual cell. To examine the histone modifications in one specific cell type, a very high number of cells and cumbersome methods of cell isolation would be required. The final epigenetic histone profile of one cell type would then be an averaged view of thousands of cells.

The team, from the Karolinska Institutet in Stockholm, Sweden, applied single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system. In doing so, they probed histone modifications characteristic of active promoters, enhancers and gene bodies, and inactive regions. The scCUT&Tag profiles “were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3, and promoter–enhancer connectivity,” the authors wrote. They also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21.

“Our method—single-cell CUT&Tag—makes it possible to examine tens of thousands of single cells at the same time, giving an unbiased view of the epigenetic information in complex tissues with unparalleled resolution,” Gonçalo Castelo-Branco, PhD, associate professor at the department of medical biochemistry and biophysics, Karolinska Institute, said. “Next, we would like to apply single-cell CUT&Tag in the human brain, both in development and in various diseases. For instance, we would like to investigate which epigenetic processes contribute to neurodegeneration during multiple sclerosis and whether we would be able to manipulate these processes in order to alleviate the disease.”