Download et al

Bioinformatic Discovery of TransposableElements
Expression in Human Cancer
1, Un-Jong Jo1,Jae-Won Huh2 and Heui-Soo Kim1, 2
Dae-Soo
Kim
Dae-Soo Kim1,Jae-Won Huh2 and Heui-Soo Kim1, 2
1PBBRC,
1PBBRC,
Interdisciplinary
Research
Program
of Bioinformatics,
CollegeCollege
of Natural
Sciences,
Pusan National
Interdisciplinary
Research
Program
of Bioinformatics,
of Natural
Sciences,
University,
PusanBusan
National University, Busan
2Division
2Division
of Biological
Sciences,
CollegeCollege
of Natural
Sciences,Pusan
National
University,
Busan Busan
of Biological
Sciences,
of Natural
Sciences,Pusan
National
University,
RESULTS & DISCUSSION
ABSTRACT
79.8%
80%
80%
70%
Percent of exons %
70%
60%
50%
40%
60%
50%
40%
30%
20%
30%
11%
6%
10%
20%
13.6%
10%
0%
3.8%
5′UTR
1.6%
0.7%
0.2%
0.1%
0.1%
4
5
6
11
17
CDS
3′UTR
Location of transposable elements fusion EST
0%
1
2
3
Transposable element fuion EST counts
Figure Transposable elements fusion EST counts
Table Distribution of transposable element family in region of transposable element exonization
Transposable elements
Transposable elements
fusion region within genes
SINE Family
LINE Family
LTR Family
619
280
85
CDS
76
30
33
5′
UTR
44
20
14
3′
UTR
Table Distribution of transposable elements
into coding and untranslated region of gene
Family
SINE Family
cancer..
LINE Family
INTRODUCTION & RESEARCH AIMS
Most of TEs are transcriptionally silent in human normal tissues,
however, some of TEs have been found to be expressed in placenta
tissues and cancer cell lines. The L1 antisense promoter-driven
transcription has been detected in human tumor cells or normal ones,
while HERV LTR elements have shown the bidirectional promoter
activity (Medstrand et al., 2001; Nigumann et al., 2002; Dunn et al.,
2003; Sin et al., 2006). Those elements could provide biological role
of organismal complexity by transcriptional diversity (Landry et al.,
2003). Here, we developed a database for understanding the
mechanism of cancer development in relation to TEs in human EST
sequences.
http://www.primate.or.kr
90%
82%
90%
Genes %
Transposable elements are the most abundant interspersed sequences
in human genome. It has been estimated that approximately 45% of
the human genome comprises of transposable elements. Most of
transposable elements are transcriptionally silent in human normal
tissues, however, some of transposable elements have been found to
be expressed in placenta tissues and cancer cell lines. Recent studies
have shown that transposable elements could affect coding sequences,
splicing patterns, and transcriptional regulation of human genes. In
the present study, we investigated the transposable elements in
relation to human cancer. Our analysis pipeline adopted for screening
methods of the cancer specific expression from human expressed
sequences. We developed a database for understanding the
mechanism of cancer development in relation to transposable
elements. Totally, 999 genes were identified to be integrated in their
mRNA sequences by transposable element. We believe that our work
might help many scientists who interested in cancer research to gain
the insight of transposable element for understanding the human
Molecular Biology & Phylogeny LAB.
LTR Family
DNA Family
Others
Subfamily
DNA Family
76
5
5
Others
1
0
0
Table 3 EST based expression profiles of
transposable elements in human cancer
Transposable elements fusion in gene region
Alu
5UTR
0
CDS
20
3UTR
0
AluJ
20
131
12
AluS
13
190
15
AluY
3
37
5
MIR
33
198
7
FAM
0
2
0
FRAM
0
16
2
FLAM
7
25
3
HAL
0
11
0
L1HS
0
1
0
L1P
1
12
5
L1M
6
125
6
L2
22
111
7
L3
1
20
2
MaLR
16
40
6
ERV1
13
23
3
ERVL
4
16
5
ERVK
0
6
0
Charlie
0
9
0
HSMAR2
0
2
0
Kanga1
0
0
1
MARNA
0
3
0
MER
5
50
3
Tigger
0
11
1
Zaphod2
0
1
0
Charlie
0
1
0
Table Potential splice site are utilized by transposable elements fusion exons
Transposable elements
Type of
potential splicing site SINE Family
LINE Family
LTR Family
Accept&Donor
83
68
50
Accept Site
271
110
33
Donor Site
216
80
43
DNA Family
12
28
18
Database Construction
MATERIALS & METHODS
SUMMARIES AND FUTURE DIRECTIONS
Through this update, we will be able to profile the patterns of
transposable expression in various diseases and to understand the
transposable element that have an effect on the expression of human
functional genes. We believe that our work will help us gain insight
into implication of TEs expression in human evolution and diseases.
REFERENCES
Kim TH, Jeon YJ, Kim WY, Kim HS: HESAS: HERVs expression and structure analysis system.
Bioinformatics 2005, 15:1699-1970.
Kim DS, Kim TH, Huh JW, Kim IC, Kim SW, Park HS, Kim HS : LINE FUSION GENES: a database
of LINE expression in human genes. BMC Genomic 2006, 7:139
Genome Information LAB & Primate & Long Terminal Repeat & Long Interspersed Nuclear Elements & Short Interspersed Nuclear Elements