Comparative Analysis of Alu Insertion Sequences in the APP 5 0 Flanking Region in Humans and Other Primates Jordi Clarimo´n, Aida M. Andre´s, Jaume Bertranpetit, David Comas Unitat de Biologia Evolutiva, Facultat de Cie`ncies de la Salut i de la Vida, Universitat Pompeu Fabra, C/ Doctor Aiguader 80, Barcelona, 08003, Catalonia, Spain Received: 11 July 2003 / Accepted: 9 December 2003 Abstract. Overexpression of the amyloid precursor protein gene (APP) may play a role in the neuropa- thology of Alzheimer’s disease. Therefore, elucidating the mechanisms involved in APP gene regulation is of primary importance, and various cis-acting regula- tory elements located in 5 0 distal regions are known to play a main role. Some of them lie within Alu ele- ments, one of which (Alu1) is only found in humans and apes while the other (Alu2) has a much older history and is also found in rhesus. These Alu inser- tions harbor sequence motifs that may act as cis- regulatory elements, which may cause differences in APP regulation among primate species and whose functionality may be ascertained through their conservation in a comparative analysis. We have performed a comparative analysis of the region comprising the two Alu elements of the APP pro- moter in several primates, including humans. We have found a significant decrease in nucleotide di- versity in the Alu2 element (inserted in all the species analyzed) compared to the Alu1 (inserted only in apes). This finding can be interpreted as a constric- tion in the Alu2 sequence variation as a consequence of a functional role of this element in the APP ex- pression. The present results suggest a wider exten- sion of the regulatory elements than the known short consensus regulatory sequences. Moreover, the different conservation of two highly similar and neighboring sequences suggests that, besides the importance of the sequence motifs, their position in relation to the gene suggests that they have played a role in being recruited as regulatory elements. Key words: Alu element — APP gene — Alzhei- mer’s disease — Promoter — Regulatory region Introduction One of the hallmarks of Alzheimer’s disease (AD) is the deposition of the 39- to 43- amino acid residue amyloid b-peptide (Ab) as a major constituent of extracellular plaques. Ab is derived from the pro- teolytic processing of the b-amyloid precursor protein (bAPP), which is encoded by the APP gene, whose overexpression has been related to the etiology of AD. Due to the evidence that a 5 0 -upstream regula- tory region of around 500 bp is sufficient for APP gene expression in cultured cells, most of the studies on APP regulation have been focused on the analysis of this proximal 5 0 -flanking region (La Fauci et al. 1989; Lahiri and Robakis 1991; Pollwein et al. 1992; Quitschke and Goldgaber 1992). However, there is also evidence that gene transcription can be greatly influenced by several positive and negative regulatory elements located upstream from this proximal region (Lahiri et al. 2000). The comparison of rhesus monkey and human APP promoters showed a region of 270 bp (posi- tions )2432 to )2161) of the human sequence that Correspondence to: Dr. David Comas; email: david.comas@upf. edu J Mol Evol (2004) 58:722–731 DOI: 10.1007/s00239-004-2594-y