Nothing beats a Pro upgrade, and lately, researchers have given CUT&Tag the deluxe treatment. This chromatin profiling method received its first improvements with the releases of scCUT&Tag and then Spatial-CUT&Tag; now, we’ve been treated to a view of the cell surface protein profile in its latest form.
A pro team of single-cell explorers from the lab of Rahul Satija (New York Genome Center) knew the obstacles on their journey to the highest peaks in the epigenetic landscape – the sparse nature of single-cell chromatin data and our inability to profile multiple histone modifications in the same cell. Fortunately, this scientific squad also knew how to move scCUT&Tag up the epigenetic ranks and reveal the epigenetic events contributing to cellular heterogeneity.
Let’s hear how Zhang and colleagues managed to turn scCUT&Tag “pro” by profiling cell surface proteins and using advanced computational analysis:
- In scCUT&Tag-pro, the integration of scCUT&Tag with cell surface proteins (e.g., CD4, CD8, CD14, and CD16) permits the simultaneous profiling of CUT&Tag profiles and cell surface protein abundance in single cells
- A shared panel of cell surface protein levels helps to integrate multiple scCUT&Tag-pro datasets, although this can extend to other epigenetic techniques to create a multimodal atlas
- The team also introduce a single-cell version of ChromHMM (scChromHMM), a downstream computational tool that integrates data from scCUT&Tag-pro experiments
- scCHromHMM can infer/annotate chromatin states over a 200 bp region, thereby generating co-assay profiles for six histone modifications within single cells
- Analysis of scCUT&Tag-pro data with scChromHMM created an integrated profile of human peripheral blood mononuclear cells (PBMNCs) as a proof-of-concept that supports the characterization of dynamic functional changes in individual genomic elements across discrete cell states/during development, the identification of the motifs and regulators establishing chromatin states, and the description of cell-type-specific regulatory priming
- The authors note substantial heterogeneity in chromatin state at stably expressed genes
- Findings include cell-type-specific repression via H3K27me3, which the authors hypothesize may represent a “priming” event for future gene repression
Now that scCUT&Tag has stepped up and turned pro thanks to a new angle of attack, the authors believe that they will be able to explore single-cell heterogeneity in detail, correlate epigenetic alterations to sequence elements, and integrate additional datasets into all-encompassing reference maps. Exciting future studies from this epigenetic ensemble will include bone marrow cell analysis to elucidate the dynamics that establish heterogeneity in circulating immune cells.
To learn more about how scCUT&Tag leveled up and turned pro, head over to Nature Biotechnology, March 2022.