Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition

Abstract

Analysis of Alu repeat distribution for the human genome build 32 (released in January 2003) reveals that they occupy nearly one-tenth portion of the sequenced regions. Huge variations in Alu frequencies were seen across the genome with chromosome 19 being the most and chromosome Y being the least Alu dense chromosomes. The highlights of the analysis are as follows: (1). three-fourth of the total genes in the genome are associated with Alus. (2). Alu density is higher in genes as compared with intergenic regions in all the chromosomes except 19 and 22. (3). Alu density in human genome is highly correlated with GC content, gene density and intron density with GC content being major deterministic factor compared with other two. (4). Alu densities were correlated more with gene density than intron density indicating the insertion of Alus in untranslated regions of exons.