Identification of fusion transcripts with retroviral elements and its application as a cancer biomarker Yun-Ji Kim 1, Jae-Won Huh 2, Dae-Soo Kim 3, Hong-Seok Ha 1, Kung Ahn 1, Ja-Rang Lee 1, Yi-Deun Jung 1, and Heui-Soo Kim 1 1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan , Republic of Korea 2 National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk , Republic of Korea 3 Korea Bioinformation Center, KRIBB, Daejeon , Korea Abstract Introduction Materials & Methods Results References The human genome is estimated to be composed of 45% transposable elements (TEs). They have been reported to have capacity for affecting adjacent genes by altering transcriptional regulation. Most TEs are transcriptionally silent in normal tissues. However, TEs have been found to be expressed specifically in cancer cell lines. Here we investigated the cancer specific fusion transcript with TEs using bioinformatics and experimental approaches. To identify the candidate cancer markers, we adopted an analysis pipeline for screening methods to detect cancer- specific expression from expressed human sequences and developed a database. Total 999 genes fused with transposable elements were found to be cancer- specific in our analysis of the EST database. To confirm the candidate marker transcripts, experimental validation was conducted by RT-PCR analysis in tumor/adjacent normal tissues and corresponding cancer cell lines. Our results could contribute greatly to understand the human cancers in relation to transposable element.…… ……...…... 1.Kim TH, Jeon YJ, Kim WY, Kim HS: HESAS: HERVs expression and structure analysis system. Bioinformatics 2005, 15: 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 Hypothetical model for retroelements in human genome Promoter region 1 exon Transcription change Supplying the Promoter or Enhancer 1 exon 2 exon Exonization in UTR and CDS region Alternative Promoter 1 exon 2 exon Alternative Polyadenylation last exon Retroelement Retroposon SINE Retrotransposon LINE RNA intermediate - LTR element+ LTR element - env+ env - RT+ RT Yeast Ty1/copia/truncated HERVs LTRORF1ORF2LTR Human THE1 P Poly(A) Human Alu ORF1ORF2P Poly(A) L1 gagpolenvLTR Full-length HERVs/exogenous retrovirus Retrovirus ′ Aims Most of TEs are tranScr- iptionally 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 develop- ment in relation to TEs in human ESTsequences, and conducted experiemental validation using RT- PCR in tumor/adjacent normal tissues and corresponding cancer cell lines to confirm the candidate marker transcripts. RT-PCR & Real-time PCR Bioinformatics NCBI,BLAST,MEGA3 Transposable elements fusion region within genesSINE FamilyLINE FamilyLTR FamilyDNA FamilyOthers CDS ′ UTR Transposable elements Table. Distribution of transposable element family in region of transposable element exonization 5 ′ UTR AKR1C2 aldo-keto reductase family 1, member C2 Chr.10 p15.1 NM_ NM_ CB LTR/MaLR MLT1L LINE/L1 LTR/MaLR MSTA 30 cycle32cycle34 cycle liver(N) liver(C) liver(N) liver(C) liver(N) liver(C) 300 bp GAPDH 120 bp NM_ NM_ AW Chr.9 q AluJo/FRAM Coding region Untranslated region colon(N) colon(C) colon(N) colon(C) tight junction protein 2 (zona occludens 2) TJP bp GAPDH 120 bp 121 Transposable elements fusion region within genesSINE FamilyLINE FamilyLTR FamilyDNA FamilyOthers CDS ′ UTR ′ UTR Transposable elements Table. Distribution of transposable element family in region of transposable element exonization Type of potential splicing siteSINE FamilyLINE FamilyLTR FamilyDNA Family Accept&Donor Accept Site Donor Site Transposable elements Table. Potential splice site are utilized by transposable elements fusion exons Experimental data tumor/adjacent normal tissues DATABASE Computational data