Correlation between Exons and Dispersed Repetitive
DNA Distribution on the Human Genome
Yoshiaki Hojo 12
Ikuo Uchiyama 2
Yataro Daigo 2
hojo@jkk.hitachi.co.jp
uchiyama@ims.u-tokyo.ac.jp
y-daigo@ims.u-tokyo.ac.jp
Yusuke Nakamura 2
Toshihisa Takagi 2
yusuke@ims.u-tokyo.ac.jp

takagi@ims.u-tokyo.ac.jp

Hitachi, Ltd. Information Systems Group. Shinsuna Plaza 6-27, Shinsuna 1-Chome,Koto-ku, Tokyo 136, Japan
2 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

1

1 Introduction

The human nuclear genome contains a large number of highly repeated DNA sequences. The Alu
sequences are primate speci c and are the most abundant family of repeated DNA sequences in thehuman genome. The human Alu sequence is approximate 300 bp long [2]. The L1 sequence is a longinterspersed nuclear element. L1 is found in other mammals. Although their functions are not yet
clear [4], some of them may a ect gene functions or cause human diseases [3].
We have identi ed repeated DNA sequences from human genomic sequences in the region of 3p21.3p22 and 9q32, both of which are more than 1M bp long. Our statistical analysis shows that thedistributions of Alus and exons have a weak positive correlation and those of L1s and exons have aweak negative correlation.

2 Method
Genomic sequence data of the human chromosome 3p21.3-p22 and 9q32 as well as cDNA sequenceson these regions were obtained by Y.Daigo et al. (unpublished data). The lengths of sequences on thechromosome 3p21.3-p22 and 9q32 are 1.2M bp and 1.0M bp respectively. While the region 3p21.3-p22
contains 14 genes, the region 9q32 has only 3 genes.
Repetitive sequences were identi ed by the computer program CENSOR [1] with Repbase(Release5.0). We divided each sequence into non-overlapping 100k bp segment and counted the exon, Alu andL1.

3 Result & Discussion
To characterize the exon, Alu and L1 distributions, we compared their densities. The Alus and exons
were more abundant in the 3p21.3-p22 region whereas the L1s were more abundant in the 9q32 region.
To test the signi cance of these di erences, we applied a statistical analysis technique known as twosample paired t-test. The signi cant di erence (p<0.05) between the regions was observed in exonand Alu but not in L1 (Table 1).
Next, densities of exon, Alu and L1 in each 100k bp segment were plotted in Fig. 1. Due toextremely low gene content, no or little tendency was observed in the region 9q32. In 3p21.3-p22,
positive correlation against exon density was observed for Alu(r = 0:42) and negative correlation
against exon density was observed for L1 (r = 00:42). When the data in both regions were taken into286

account, the correlation coecient between exon and Alu densities became 0.62 while that between
exon and L1 densities was unchanged (r = 00:42). However, when the segment size was enlarged up
to 170k bp, the latter correlation coecient also became a large negative value 00:7 (data not shown).
These results suggest that Alu
elements but not L1s have a tenTable1:Comparison of exon, Alu and L1 density
dency to cluster into regions whereexon
AluL1
the gene density is high. Although
3p21-22(1/k bp)
0.15
0.34
0.12
existence of direct relationships be9q32(1/k bp)
0.02
0.16
0.16
tween exons and repetitive elements
Std.
0.12
0.13
0.11
is not clear yet, the observed corret
3.28
4.78 00:89
lations might have an in uence onp1.721003 4.521005
0.20gene function or gene expressions.

:A, Correlation between Alu density and Exon density. Correlationcoecient is 0.62. B, Correlation between L1 density and exon
density. Correlation coecient is 00 42. Squares are 3p21.3-p22.
Diamonds are in 9q32.

Figure 1: Correlation between exon density and Alu or L1

exon/kb287[4] Schmid, C.W., Dose SINE evolution preclude Alu function, Nucl. Acids Res., 26(20):4541{4550,1998.

[3] Mighell, A.J., Markham, A.F., Robinson, P.A., Alu sequences, FEBS Letters., 417:1{5, 1997.

[2] Kariya, Y., Kato, K., Hayashizaki, Y., Himeno, S., Tarui, S., Matsubara, K., Revision of consensus
sequence of human Alu repeat { a review, Gene, 53:1{10, 1987.

[1] Jurka, J., Klonowski, P., Dagman, V., Pelton, P., CENSOR - a program for identi cation andelimination of repetitive element from DNA sequence, Comp. Chem., 20(1):119{122, 1996.

References

This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas, `GenomeScience', from the Ministry of Education, Science, Sports and Culture of Japan.

Acknowledgments

exon/kb