abstract

ABSTRACTTransposable 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..

INTRODUCTION & RESEARCH AIMSMost 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.

MATERIALS & METHODS

SUMMARIES AND FUTURE DIRECTIONSThrough 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.

RESULTS & DISCUSSIONhttp://www.primate.or.kr

REFERENCESKim 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 databaseof LINE expression in human genes. BMC Genomic 2006, 7:139

13.6%

3.8%1.6% 0.7% 0.2% 0.1% 0.1%

79.8%

0%

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90%

1 2 3 4 5 6 11 17

Transposable element fuion EST counts

Gen

es %

Figure Transposable elements fusion EST counts

11%

82%

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5′UTR CDS 3′UTR

Location of transposable elements fusion EST

Per

cent

of

exon

s %

Transposable elements fusion region within genes SINE Family LINE Family LTR Family DNA Family Others

CDS 619 280 85 76 1

5′UTR 76 30 33 5 0

3′UTR 44 20 14 5 0

Transposable elements

Table Distribution of transposable element family in region of transposable element exonization

5UTR CDS 3UTR

Alu 0 20 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

Others Charlie 0 1 0

Transposable elements fusion in gene region

DNA Family

LTR Family

LINE Family

SINE Family

Family Subfamily

Table Distribution of transposable elements into coding and untranslated region of gene

Table 3 EST based expression profiles of transposable elements in human cancer

Type of

potential splicing site SINE Family LINE Family LTR Family DNA FamilyAccept&Donor 83 68 50 12Accept Site 271 110 33 28Donor Site 216 80 43 18

Transposable elements

Table Potential splice site are utilized by transposable elements fusion exons

Database Construction

Dae-Soo Kim1, Un-Jong Jo1,Jae-Won Huh2 and Heui-Soo Kim1, 2

1PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan2Division of Biological Sciences, College of Natural Sciences,Pusan National University, Busan

http://www.primate.or.kr/

Dae-Soo Kim1,Jae-Won Huh2 and Heui-Soo Kim1, 2

1PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan2Division of Biological Sciences, College of Natural Sciences,Pusan National University, Busan

Bioinformatic Discovery of TransposableElements Expression in Human Cancer

Molecular Biology & Phylogeny LAB.

Genome Information LAB & Primate & Long Terminal Repeat & Long Interspersed Nuclear Elements & Short Interspersed Nuclear Elements