Association of some potential hormone response elements in human genes with the Alu family repeats

Short interspersed repeats of the Alu family located in promoters of some h uman genes contain high-affinity binding sites for thyroid hormone receptor , retinoic acid receptor and estrogen receptor. The standard binding sites for the receptors represent variants of duplicated AGGTCA motif with differ ent spacing and orientation (direct, DR, or inverted, IR), and Alu sequence s were found to have functional DR-4, DR-2 or variant IR-3/IR-17 elements. In this study we analyzed distribution and abundance of the elements in a s et of human genomic sequences from GenBank and their association with Alu r epeats. Our results indicate that a major fraction of potentially active DR -4, DR-2 and variant IR-3/IR-17 elements in the genes is located within Alu repeats. Alu-associated DR-2 elements are conserved in primate evolution. However, very few Alu have potential DR-3 glucocorticoid-response elements. Gel-shift experiments with the probe (AUB) corresponding to the consensus Alu sequence just upstream of the RNA polymerase III promoter B-box and con taining duplicated AGGTCA motif indicate that the probe interacts in a sequ ence-specific manner with human nuclear proteins which bind to standard IR- 0, DR-1, DR-4 or DR-5 elements. The AUB sequence was also able to promote t hyroid hormone-dependent trans-activation of a reporter gene. The results s upport the view that Alu retroposons played an important role in evolution bf:regulation of the primate gene expression by nuclear hormone receptors. (C) 1999 Elsevier Science B.V. All rights reserved.