Table 1 Parameters and range of empirical estimates for our population-genetic model of binding site evolution
ParameterMeaningValue range
μPer-nucleotide per-generation mutation rate10−7−10−9 per generation (Drake et al. 1998; Lynch 2010)
KNumber of true targets: genomic positions at which selection favors a functional binding site100−103 binding sites (Lee et al. 2002; Münch et al. 2003; Harbison et al. 2004; Teixeira et al. 2006; Gama-Castro et al. 2011)
LNumber of false targets: genomic positions at which selection disfavors a functional binding site105−107 binding sites (for a genome with 103−105 genes) (Lynch and Conery 2003)
nBinding-site length5−40 nt (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
rBinding degeneracy: the average number of different bases at each nucleotide that produce functional binding1.0−4.0 bases (empirical mean = 1.6 bases) (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
IAverage information content per nucleotide in a binding site, Embedded Image0.25−2 bits (empirical mean = 1.3 bits) (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
NEffective population size104−107 individuals (Lynch 2010)
Ns+Strength of selection on true targets∼10 (Mustonen et al. 2008; He et al. 2011)
NsStrength of selection on false targets≲1 (Hahn et al. 2003)
PNumber of TF proteins in a cell100−103 (Thattai and Van Oudenaarden 2001; Gerland et al. 2002)
εMismatched nucleotide binding energy contribution1−3 (units of kBT) (Gerland et al. 2002; Lässig 2007)