While we’re usually fans of shortcuts that make our lives easier, this exciting combination of accessible methods to profile single-cell chromatin modifications has our attention, no matter how you slice it.
Chromatin profiling using cleavage under targets and tagmentation (CUT&Tag) allows you to investigate histone post-translational modifications and transcription factor occupancy, particularly when limited by the number of cells available. In this latest technological breakthrough, researchers from Goncalo Castelo-Branco’s lab (Karolinska Institutet, Sweden) combined CUT&Tag technology with 10x Genomics’ Chromium droplet-based single-cell technology to characterize chromatin modifications at the single-cell resolution. Their method works with single nuclei and relies on an antibody binding to a target transcription factor or histone post-translational modification, but instead of immunoprecipitation, chromatin shearing and library prep are achieved thanks to the recruitment of a protein A-Tn5 transposase fusion by a secondary antibody. Let’s cut to the chase:
- Single-cell CUT&Tag (scCUT&Tag) works with thousands of cells from the mouse central nervous system by combining CUT&Tag and a single-cell ATAC-seq protocol
- Active regions (H3K4me3, H3K27ac, H3K36me3) and inactive regions (H3K27me3) can be probed
- These profiles sufficiently determine cell identity between mouse embryonic stem cells, fibroblasts, and oligodendrocyte progenitor cell line
- Cell populations in developing mouse brain can be identified based on H3K4me3, H3K27ac, and H3K27me3, which enables the distinction between mature oligodendrocytes, astrocytes, olfactory ensheathing cells, vascular cells, oligodendrocyte progenitors, excitatory neurons, inhibitory neurons, and microglia
- Three regulatory principles can be deconvoluted based on the combinatorial profiles:
- Promoter H3K4me3/H3K27me3 bivalency: as H3K4me3 is enriched, H3K27me3 is depleted
- Spreading of H3K4me3: while oligodendrocytes differentiate, H3K4me3 spreads
- Promoter-enhancer connectivity: an activity-by-contact model can predict enhancer-promoter interactions, consistent with bulk CUT&Run data, with as few as 100 cells, most specifically for oligodendrocytes
- Application of scCUT&Tag to assess the chromatin occupancy of transcription factors OLIG2 (oligodendrocytes) and RAD21 (ubiquitous expression) enables the distinction of cell identity
First author Marek Bartosovic explained, “This technique will be an important tool for examining what makes cells different from each other at the epigenetic level. We anticipate that it will be widely implemented by the broad biomedical community in a wide variety of research fields.”
Lead investigator Goncalo Castelo-Branco added, “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. 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.”
See what makes this work a cut above in Nature Biotechnology, April 2021.