The title of yet another paper speaks for itself: Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes (Paz Polak and Eytan Domany. BMC Genomics. 2006; 7: 133).
Let’s look at the abstract.
This research suggests that evolution used transposable elements to insert modules of transcription factor binding motifs into promoters and, by means of their presence, assemble higher level regulatory networks. In order to explore this question we focused on Alu elements, which are good potential candidates to be part of the building blocks of regulatory networks for two reasons. First, Alu elements are abundant in the upstream region of the TSS of genes, and second, Alu elements contain dozens of putative BSs for TFs. Some of these BSs were found before and their association with Alu was also reported, whereas in some cases although the BSs were found, the fact that they reside on Alu went unnoticed. Finally, we list here also BSs on Alu that were not identified previously. Our findings imply that the biological pathway on which Alu-mediated regulation appears to have the most significant impact is the development process. Many of the TFs that have binding motifs on Alu are associated with development; moreover, some of these BSs were previously demonstrated to be functional in vivo and essential to regulation of some target genes.
TF stands for transcription factors, proteins that bind to specific DNA sequence to activate the process of gene expression. TSS stands for transcription start site, the precise point at which the copying of the DNA into an RNA format begins. BS stands for binding site, the region of the DNA that binds with the transcription factors.
Given that Alu elements contain so many potential binding sites for so many genes involved in stress response, blood formation, heart development, muscle development, brain development, eye development, pancreas developments, overall embryonic development, and sterol biosynthesis, their ability to reformat the genome, and its developmental programs, make them a very powerful tool for evolution. And to think they were once dismissed as junk DNA.