In Silico Analysis of Transposable Elements Expression in

In Silico Analysis of Transposable Elements Expression in Human Cancer 1, Un-Jong Jo 1, Jae-Won Huh 2 and Heui-Soo Kim 1, 2 Dae-Soo Kim 1, Un-Jong Jo 1, Jae-Won Huh 2 and Heui-Soo Kim 1, 2 1 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National Interdisciplinary Research Program of Bioinformatics, of Natural Sciences, University, Pusan. Busan National University, Busan 2 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan of Biological Sciences, of Natural Sciences, Pusan National University, 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 m. RNA 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 http: //www. primate. or. kr / Molecular Biology & Phylogeny LAB. RESULTS & DISCUSSION http: //www. primate. or. kr 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. . 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 L 1 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. 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