In Silico Analysis of Transposable Elements Expression in Human Cancer

1. 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 ATGCA AT In Silico Analysis of Transposable Elements Expression in Human Cancer Genome Information Lab http://www.primate.or.kr/ Molecular Biology & Genome Information Lab. http://www.primate.or.kr RESULTS & DISCUSSION ABSTRACT 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 elements within cancer specific expression transcripts 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. Table Distribution of transposable elements into coding and untranslated region of gene Human Endogenous Retrovirus (HERV) & Long Terminal Repeats (LTR) Long Interspersed Nuclear Elements (LINE) & Short Interspersed Nuclear Elements (SINE) Table. EST based expression profiles of transposable elements in human cancer Database Construction MATERIALS & METHODS 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.

2. Figure Transposable elements fusion EST counts Table Distribution of transposable elements into coding and untranslated region of gene Table 3 EST based expression profiles of transposable elements in human cancer 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