Relationship between Chromosome Rearrangement and
Repeat Sequences in Human Chromosome 7
1
Hiroo Murakami1
Nobuyoshi Sugaya1
[email protected]
[email protected]
Sachiyo Aburatani1
Katsuhisa Horimoto1
[email protected]
[email protected]
Laboratory of Biostatistics, Institute of Medical Science, University of Tokyo,
4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
Keywords: chromosome rearrangement, periodic sequence, tandem repeat, dispersed repeat, STEPSTONE
1
Introduction
A various types of repeat patterns are abundant in genomic sequence, and are associated with the biological
phenomena at distinct levels. In particular, comparative analyses of whole-genome-sized sequence data
reveal that the periodic sequences cause the segmental duplication that is a type of chromosomal structural
arrangement [2]. In this study, we analyze the relationships between the large-scale segmental duplication of
chromosome and the periodic sequences. For this purpose, the periodic sequences are detected by three tools
to detect repeats of genomic sequence, and the distribution of detected periodic sequences is corresponded
with the locations on the chromosome where the segmental duplications are observed.
2
2.1
Methods and Results
Data
We analyze human chromosome 7 genomic sequence (153794793 bp, GenBank accession: BL000002,
version 020621) [3]. In addition to the original sequence (‘repeat-unmasked’), we also analyze a processed
sequence (‘repeat-masked’) [3]; dispersed repeat elements such as Alu element and simple repeats with a few
base periods are removed from the original sequence by Repeat-masker [6].
The locations of segmental duplication of self- or other- chromosome of chr. 7 are identified from PDF file
(>90% sequence identity and >1kb length) [3]; the file is converted to high-resolution bit-map, in which one
dot corresponds to 29289 bp in the genomic sequence.
2.2
Methods for Detecting Repeat Sequences
The repeat patterns are detected by execution of three repeat-finding programs without a priori knowledge,
Tandem Repeat Finder (TRF) [1], mreps [4], and STEPSTONE [5], in both "repeat-masked" and
"repeat-unmasked" chr. 7 sequences. The distribution of detected repeat patterns is compared with the
locations of segmental duplications of self- or other- chromosomes.
2.3
Relationship between Chromosome Rearrangement and Distribution of Repeat Sequences
Many periodic patterns with large periodicity appeared around the telomere regions and near in the region of
segmental duplication (Fig. 1). In the ‘un-masked’ sequence, STEPSTONE detects periodic patterns with the
large periods, Mreps detects periodic patterns with short periods, and TRF detects patterns with the middle
range of periods. Interestingly, all tools commonly detect the periodic sequences around the location of
60,000,000 bp where a huge segmental duplication is observed.
In the ‘repeat-masked’ sequence, both TRF and STEPSTONE detect periodic patterns with large
periodicity around the segmental duplication region. This suggests that unknown periodic sequences with
large periodicity are related with the segmental duplication.
TRF
(unmasked)
mreps
(unmasked)
STEPSTONE
(unmasked)
TRF
(masked)
STESPTONE
(masked)
1
153794793 (bp)
Figure 1: Correspondence between the periodic sequences detected by TRF, mreps, and STEPSTONE, and
the locations of segmental duplications in human chromosome 7. In the graph, the horizontal axis is location
of the genomic sequence, and the vertical axis is periodicity. The vertical lines in the graph indicate the
locations of segmental duplications: light-colored lines are self-chromosomal duplications and dark-colored
lines are other-chromosomal duplications.
3
Discussion
By picking up the periodic patterns of ‘repeat-masked’ sequences in which the segmental duplications are
observed, we reveal novel periodic patterns in the segmental duplication region. In further study, we will
characterize the periodicity of repeat patterns by statistical tests.
References
[1] Benson, G., Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res.,
27(2):573-80, 1999.
[2] Eichler, E.E. and Sankoff, D., Structural dynamics of eukaryotic chromosome evolution, Science,
301:793-797.
[3] Hillier, L.W., Wilson, R.K., et al., The DNA sequence of human chromosome 7, Nature, 424:157-164.
[4] Kolpakov, R., Bana, G. and Kucherov, G., mreps: efficient and flexible detection of tandem repeats in
DNA, Nucleic Acids Res., 31:3672-6378, 2003.
[5] Murakami, H., Sugaya, N., Sato, M., Imaizumi, A., Aburatani, S. and Horimoto, H., Detection of
inter-spread repeat sequence in genomic DNA seaquence, Genome Informatics, 15(1):170-179, 2004.
[6] http://ftp.genome.washington.edu/RM/RepeatMasker.html