Increased concentration of some transcription factor binding sites in human retroposons of the Alu family

Eukaryotic gene expression is dependent on short protein-binding DNA sequence motifs promoting the assembly of multiprotein transcription complexes. Human retroposons of theAlu family are known to contain some high-affinity binding sites for transcription factors, which may serve as signals in regulation of expression of RNA-polymerase II-transcribed genes. In this computer study we have compared the density of ten consensus transcription factor binding sites in a set of human mature mRNA, human promotors andAlu repeats. Our results indicate thatAlu retroposons and promotor sequences have significantly higher mean density of these sites compared to RNAs. It is suggested that the majority ofAlu repeats do have the potential for regulating gene expression via modulation of RNA polymerase II-dependent transcription.