Relationship between Segmental Duplications and Repeat Sequences in Human Chromosome 7

Hiroo Murakami (hiroo@ims.u-tokyo.ac.jp)
Sachiyo Aburatani (sachiyo@ims.u-tokyo.ac.jp)
Katsuhisa Horimoto (khorimot@ims.u-tokyo.ac.jp)

Laboratory of Biostatistics, Institute of Medical Science, University of Tokyo, Shirokane-dai 4-6-1, Minato-ku, Tokyo 108-8639, Japan


Abstract

Various types of repeat sequences are abundant in genomic sequences, and they are associated with the biological phenomena at distinct levels. In particular, comparative analyses of whole-genome-sized sequence data have revealed that repeat sequences cause segmental duplications, which are a type of chromosomal structural arrangement. In this study, we analyzed the relationships between segmental duplications and repeat sequences in human chromosome 7. For this purpose, three methods for detecting repeat sequences were applied to the genomic sequences of human chromosome 7: RepeatMasker for the dispersed repeats, TRF for the tandem repeats, and STEPSTONE for the inter-spread repeats. By plotting the detected repeat sequences against the locations on the chromosome, all three types of repeats were found to be concentrated around the regions of segmental duplications, as a macroscopic feature of their distributions. Furthermore, the latter two repeat sequences were classified in terms of their periods, and the distribution bias of the detected repeat sequences was statistically tested between the segmental duplication regions and the other regions. As a result, the periods of two repeats were biased, with less than a 5% level of significance probability by the χ2 test, and the repeats with long periods, about 130bp and more than 400bp, were attributed to a bias with a 5% level of significance probability by the normalized residual test. The mechanism of segmental duplications is discussed based on the present results.

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Japanese Society for Bioinformatics