A mathematical approach to predict the affinity of estrogen receptors alpha and beta binding to DNA.

Estrogen receptors alpha and beta (ERalpha and ERbeta) bind to specific DNA sequences, estrogen response elements (EREs), usually located in the promoters of estrogen-regulated genes. The consensus ERE contains two inverted repeats of the 5'-AGGTCA-3' half-site (1/2 ERE) separated by three base pairs (bp). Many estrogen-responsive gene promoters contain one or more direct repeats (DR) of 1/2 ERE. Here, we examined the affinity of ERalpha and ERbeta binding and estradiol (E(2))-induced transactivation from select EREs and DRs. The affinity of ERalpha and ERbeta binding to imperfect EREs in vitro can be predicted from equations using the number of 1/2 EREs and the number of (AT)-(GC) bp substitutions within the 15-bp candidate ERE sequence as independent variables. Transactivation by ERalpha and ERbeta correlates with the affinity of ER-ERE binding with the exception of ERalpha from two low-affinity EREs. The equations developed here can be used to screen the promoters of estrogen-responsive genes for candidate ERE sequences.