Epistasis facilitates functional evolution in an ancient transcription factor

A protein’s genetic architecture – the set of causal rules by which its sequence determines its specific functions – also determines the functional impacts of mutations and the protein’s evolutionary potential. Prior research has proposed that proteins’ genetic architecture is very complex, with pervasive epistatic interactions that constrain evolution and make function difficult to predict from sequence. Most of this work has considered only the amino acid states present in two sequences of interest and the direct paths between them, but real proteins evolve in a multidimensional space of 20 possible amino acids per site. Moreover, almost all prior work has assayed the effect of sequence variation on a single protein function, leaving unaddressed the genetic architecture of functional specificity and its impacts on the evolution of new functions. Here we develop a new logistic regression-based method to directly characterize the global causal rules of the genetic architecture of multip..., , , # Epistasis facilitates functional evolution in an ancient transcription factor

This directory contains initial and intermediate datasets computed by the analysis pipeline. All .rda files can be loaded into R or RStudio.

## Description of the data and file structure

Initial Data Files

AA.SEQ.rda - Sequence code for every genotype. Row names are the sequence, with the RE listed at the beginning (E: ERE, S: SRE). Columns 1-5 give the RE or amino acid state for each site (X1-X4). Remaining columns are indicator variable for the amino acid states at each site (1: present, 0:absent)

DT.11P.CODING.rda - Initial data file from Starr et al. 2017. Contains genotype sequence; normalized counts of each genotype in each sorting bin for each RE for two replicates (RE, replicate, bin); estimate of number of colony forming units for each genotype, sorting bin, RE, and replicate; estimate of mean fluorescence for each replicate and an estimate based on combining replicates; class (null, weak, s...