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MBE Advance Access published online on June 27, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg153
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted April 17, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Non-Random Distribution of Alu Elements in Genes of Various Functional Categories: Insight from Analysis of Human Chromosomes 21 and 22

Deepak Grover 1, Partha P. Majumder 2, Chandrika B. Rao 1, Samir K. Brahmachari 1, and Mitali Mukerji 1*

1 Functional Genomics Unit, Institute of Genomics and Integrative Biology (formerly Centre for Biochemical Technology), (CSIR), Mall Road, Delhi, India
2 Anthropology and Human Genetics Unit, Indian Statistical Institute, B.T. Road, Kolkata 700 108, India

* To whom correspondence should be addressed. E-mail: mitali{at}cbt.res.in.


  Abstract

The first draft of the human genome has revealed enormous variability in the global distribution of Alu repeat elements. There are regions such as the four homeobox gene clusters, which are nearly devoid of these repeats that contrast to repeat dense regions in other transcriptionally active regions of the genome. Our analysis of the completely sequenced chromosomes 21 and 22 reveal a striking bias in Alu distribution. These elements are more clustered in genes which are involved in metabolism, transport and signalling processes. In contrast, they are significantly lower in genes coding for information pathway components as well as structural proteins. This bias in Alu distribution, is independent of the effect of Alu density of the flanking genomic region and is also not affected by the GC content of the gene and its upstream and downstream regions. The relative proportions of Alu subfamilies (Alu J, Alu S and Alu Y) are not significantly different in genes with high Alu density belonging to the functional categories of transport, metabolism and signalling. However, in the structural proteins and information genes these proportions are lower than other three categories. We suggest that Alus might be involved in regulatory mechanisms and are therefore differentially selected in primate genomes.

Key Words: Alu, repeat distribution, chromosome 21 and 22, functional classification, retrotransposons, gene regulation


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