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Bioinformatics Advance Access originally published online on January 29, 2004
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Bioinformatics 20(6) © Oxford University Press 2004; all rights reserved.

Discovery Note

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

Deepak Grover 1, Mitali Mukerji 1, Pankaj Bhatnagar 1, K. Kannan 2 and Samir K. Brahmachari 1,*

1 Functional Genomics Unit, Institute of Genomics and Integrative Biology (IGIB), CSIR, Mall Road, Delhi 110007, India and 2 School of Biotechnology, GGS Indraprastha University, Delhi 110 006, India

Received on August 31, 2003 ; accepted on October 31, 2003
Advance Access Publication January 29, 2004

Motivation: Transposon-derived Alu repeats are exclusively associated with primate genomes. They have gained considerable importance in the recent times with evidence of their involvement in various aspects of gene regulation, e.g. alternative splicing, nucleosome positioning, CpG methylation, binding sites for transcription factors and hormone receptors, etc. The objective of this study is to investigate the factors that influence the distribution of Alu repeat elements in the human genome. Such analysis is expected to yield insights into various aspects of gene regulation in primates.

Results: 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.

Supplementary information: Online supplementary data is available at the web page http://www.igib.res.in/manuscriptdata/aluanalysis.html

Contact: skb{at}igib.res.in

* To whom correspondence should be addressed.


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