How to interpret the TF footprint plot?

Analyzing scATAC-seq data with the Signac toolkit is fascinating because it allows us to obtain several interesting results. Among these, I find the results from TF footprint analysis extremely useful because they allow us to probabilistically estimate the activity of various transcription factors without having to perform multiple ChIP-seq experiments. In this context, ChIP-seq could be used later to validate the actual activity of specific transcription factors that the footprint analysis suggests may be active in certain samples or conditions. However, interpreting footprint plots can be challenging, so today I want to clarify how to interpret these types of results. But first, let’s review some biological and computational context.

Biological Context:

scATAC-seq data consist of DNA fragments generated by cuts from the Tn5 transposase. This enzyme tends to cut in accessible regions of the chromatin, where the DNA is not compacted or bound by proteins like histones. When a transcription factor (TF) binds to a specific DNA region, that region becomes less accessible to Tn5, as the TF physically occupies the binding site and shields it from cuts.