What can we "see" with single cell ATAC-seq data ? (e.g. cell cycle - possible or not ? )

Question

[Alexander]

It seems we can see cell types with the single cell ATAC-seq data. (See the figure below - data from the ongoing Kaggle challenge: https://www.kaggle.com/code/alexandervc/mmscel-atac-seq-eda-01-dimred-visualizations?scriptVersionId=105765396&cellId=17 )

What is the other biology we can see with scATAC-seq ? And vice versa - difficult to see ? Can we see cell cycle phases for example ? (Googling did not help me). Degree of "stemness" ?

PS What seems surprising for me that cell types seems to be seen more clearly via ATAC-seq data, rather than via scRNA-seq data. Is it always the case ?

[ATpoint]

There is quite is stack of literature demonstrating that separation of cell types is more "clear" with epigenomic rather than transcriptomic data. See for example the early scATAC-seq papers by Buenrostro and colleagues. That is mainly because regulatory elements that are being probed by ATAC-seq are more celltype-specific than gene expression alone. Imagine that the same gene can be regulated by a variety of factors, say promoter or distal regulatory element accessability, or different regulatory elements, or methylation. This all channels into the same gene, but upstream regulation can be different, hence more celltype-specific than the gene expression (so the final product) alone. With regard to what you can see I have to defer to people with hands-on experience, unfortunately scATAC-seq did not cross my hands-on path by now.