@InnesBT This review paper by Gasperini, Tome, and Shendure is pretty good for the biology and protocols you can use for answering questions like this:
https://www.nature.com/articles/s41576-019-0209-0
It covers a lot o protocols and methods (#MPRA, #CRISPR screens, #eQTLs, #scRNA-seq, etc), but it doesn't focus as much on the computational construction of those things.
In this Review, Gasperini, Tome and Shendure discuss the evolving definitions of transcriptional enhancers, as well as diverse modern experimental tools to identify them. The authors describe how these diverse mindsets and methods provide differing but complementary insights into enhancers, each with notable strengths and caveats. They discuss how such views and approaches might be combined in a comprehensive catalogue of functional enhancers.
We investigated #GxE for caffeine in vascular endothelial cells with a #MPRA for >40,000 genetic variants, characterized the regulatory activity response, and linked them to cardiovascular health.
We characterized the TFs for response to caffeine, identified >7,000 GxE, validated fine-mapped eQTLs in artery and characterized mechanisms for the role of #caffeine in #cardiovascular disease.
James Hawley, PhD
Roger Pique-Regi