Transcript 2007.6.DS

In Silico Analysis of Transposable Elements Expression in Human Cancer
Dae-Soo Kim1, Jae-Won Huh2 ,Hong-Seok Ha1, Kung Ahn1, Yun-Ji Kim1, Ja-Rang Lee1, and Heui-Soo Kim1, 2
1PBBRC,
Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences,
Pusan National University, Busan
2Division of Biological Sciences, College of Natural Sciences,Pusan National University, Busan
Molecular Biology
&
Genome Information Lab.
http://www.primate.or.kr
RESEARCH AIMS
MATERIALS & METHODS
82%
80%
80%
70%
Percent of exons %
70%
60%
50%
40%
30%
60%
50%
40%
30%
20%
20%
13.6%
11%
6%
10%
10%
3.8%
1.6%
0.7%
0.2%
0.1%
0.1%
4
5
6
11
17
0%
0%
1
2
3
5′UTR
CDS
3′UTR
Location of transposable e le me nts fusion EST
Transposable element fuion EST counts
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
Table Distribution of transposable elements into coding and untranslated region of gene
Family
SINE Family
LINE Family
LTR Family
DNA Family
Others
Subfamily
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
Others
1
0
0
Table. EST based expression profiles of transposable elements in human
cancer
Transposable elements
Family
Subfamily
Alu
AluJ
AluS
SINE
MIR
FAM
FRAM
FLAM
HAL
L1HS
L1P
LINE
L1M
L2
L3
MaLR
ERV1
LTR
ERVL
ERVK
Charlie
HSMAR2
Kanga1
DNA
MARNA
MER
Tigger
Zaphod2
Charlie
Others
Occurrences
Percent (%)
20
171
244
250
2
18
37
13
1
18
153
151
25
67
40
27
6
9
2
1
3
61
14
1
1
1.44
12.35
17.62
18.05
0.14
1.30
2.67
0.94
0.07
1.30
11.05
10.90
1.81
4.84
2.89
1.95
0.43
0.65
0.14
0.07
0.22
4.40
1.01
0.07
0.07
Database Construction
SUMMARY
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.
& L o n g Te r m i n a l R e p e a t s ( LT R )
& Short Interspersed Nuclear Elements (SINE)
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.
90%
79.8%
DNA Family
76
5
5
Table. Distribution of transposable elements within cancer specific expression transcripts
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 cancer.
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
Human Endogenous Retr ovir us (HERV)
Long Interspersed Nuclear Elements (LINE)
ABSTRACT
RESULTS & DISCUSSION
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
Subfamily
SINE Family
LINE Family
LTR Family
DNA Family
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
Others
DNA Family
76
5
5
Others
1
0
0
Table 3 EST based expression profiles of
transposable elements in human cancer
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