BMC Genomics 2006, 7:133 http://www.biomedcentral.com/1471-2164/7/133 Table 4: List of biological processes whose regulation involves transcription factors with putative target sites on Alu. Those transcription factors that were experimentally found to bind to Alu (see Table 2) are in bold. These reported binding events involved specific Alu sequences, and were not based on genome-wide screening. Biological Porcess Nuclear factors and stress response Hematopoietic differentiation Heart development/Muscle development Brain and CNS development: Eye development Pancreas developments Embryonic development Sterol biosynthesis Interferon The distribution of transposable elements in the 5' upstream regions of human genes The distribution of transposable elements in the 5' upstream regions of human genesis not uniform. We computed the density of different transposable elements on 5000 bp long upstream sequences of about 14000 genes. In the region between 2000 bp and 5000 bp from the transcription start site (TSS), 45% of the nucleotides belong to transposable elements. This fraction is the same as the overall density in the entire genome – see Fig 1. In contrast, in the region closer to the TSS, between 0 and 2000 bp – the density of transposable elements is lower. The Alu density exhibits a more interesting behaviour; for short distances – between 0 and 600 bp – it is lower than the genomic average of about 10%. This is not surprising since the immediate proximal region to the TSS is rich with important binding sites for initiating factors and insertion of Alu and other transposable elements in this region is most probably selected against. The density increases steadily till about 2000 bp, where it reaches a level of 18% of the base pairs [Fig. 1], after which it main- tains a steady level (and has to decrease to the genomic average as we move further away into the intergenic region). The Alu content in the deep intergenic spacer regions is less than 10%; hence the density of on-Alu BSs in these regions is also lower than in the upstream 5000 bp regions of genes. The presences of less BSs in these regions might imply less functional relevance. Finally, 85% of the genes in our database contained at least one Alu insertion in the 5 Kbp upstream region. Non random distribution of Alu elements on promoter regions of different gene groups We analyzed the distribution of Alu elements in the 5000 bp upstream regions of genes, treating separately groups of genes that belong to different biological processes. Pro- tein biosynthesis genes are enriched with Alu compared to the genome-wide average value of 3.63 copies in the 5000 BM(TFs) ER.01–2 (see table 2), RAR.01 (table 2), LXRE.01, GC.01 (SP1) GFI.01 (Gfi-1*) LYF1.01 (ZNF1A1), GATA3.02 (GATA3), OC2.01 (ONECUT2), GATA2.01(GATA2) PITX2*, NKX25.01 (Nkx2.5*), LUN01_01(LUN1) MEF2.01–04 (MEF2A,B,C,D), RSRFC4.01/02 PAX6.01 (PAX6),PAX4.01 (PAX4), OTX2.02 (OTX2), NRL.01 (NRL), BRN2.03, (POU3F2), BRN3.01(POU3F3) PITX2.Q2 (PITX2)*,PAX6.01 (PAX6), SIX3.01(SIX3) PAX6.01(PAX6), PDX1.01 GSC.01 (GSCL) SREBP.03 (SREBPF3) IRF1.01 (IRF1) IRF2.01,(IRF2), HEN1.01, HEN1.03 (TCF1,TCF2) bp long upstream regions (Table 5). In contrast, genes that are related to various kinds of developmental processes, tissue formation (such as cell communication, central nervous system development genes and muscle develop- ment genes) contain a smaller number of Alu elements in their 5000 bp upstream region than the average value (see Table 5). Many of these differences between the Alu con- tent of genes of a particular biological process and the Alu content of the entire genome (in the 5 Kbp upstream regions) were found (by t-test) to be highly significant (Table 5). As mentioned above, similar differences in Alu content were reported [12] when the full length gene sequences on chromosomes 21 and 22 were analyzed. Studying BS content in specific (non-consensus) Alu elements in the promoter regions Hundreds of thousands of putative BSs reside on Alu ele- ments in the upstream regions of genes. For several TFs one observes that nearly all the putative BSs (more than 90%) are located on Alu. The search for BMs presented in the previous sections was done on the consensus sequences of various Alu subfamilies. Since, however, Alu elements have mutated after insertion, there is considera- ble deviation from the consensus in the specific Alu sequences that are found across the genome. This varia- tion may change the BS content of specific individual Alu elements versus the consensus. Hence we repeated our search of BSs in the actual 5000 bp upstream regions of about 14,000 genes, and if a BS passed a significance filter, we checked whether it resides on a specific Alu. This search was limited to those 66 BMs that passed our filter based on the consensus sequences, i.e. their largest score, Tmax, exceeded T5 for the consensus of at least one of the eight Alu subfamilies studied. For each of these 66 BMs we searched the 14,000 upstream regions for putative BMs whose score exceeds (the consensus-based) Tmax. Page 6 of 15 (page number not for citation purposes)