Introduction
Binding site discovery:
-Computational -Experimental
Cis-regulatory evolution
Organisms
-Yeast
-Fly
-Mouse
-Human
Binding site degeneracy
Functional variants
Cis-regulatory code
Regulatory networks

Gene expression regulation is fast becoming one of the most studied topics in many fields of biology, including genetics, cancer biology, and evolutionary biology because it provides an essential link between genotype and phenotype. Perhaps the most difficult aspect of understanding gene expression regulation is deducing the complex function of non-coding regions that control expression, such as transcription factor (TF) binding sites. Gene expression is controlled by TFs that bind to cis-regulatory sites in a gene’s promoter. One of the central challenges for evolutionary genomics is to determine how changes in genome sequence translate into changes in expression phenotype.

This is a guide to help myself and others navigate resources in this exciting field. It is a work in progress, and certainly under construction, so please let me know of any suggestions. Email suggestions to jrest at uchicago dot edu.