Expression of alternative transcription including LTR12C in human CHM gene in colorectal cancer Yi-Deun Jung1, Jae-Won Huh1,2, Dae-Soo Kim3, Hong-Seok Ha1 and Heui-Soo Kim1 1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea 2 National Primate Research Center, KRIBB, Ochang, Chungbuk 363-883, Republic of Korea 3 Korea Bioinformation Center, KRIBB, Daejeon 305-806, Republic of Korea http://www.primate.or.kr Abstract CHM (Choroideremia) is indispensable for the posttranslational activation of retina-specific Rab protein. Various mutations such as missense, nonsense, rearrangement of the CHM gene are responsible for choroideremia. We could find several elements including MIR, LINE, Alu and LTR12C that are located within the intron 4 of the CHM gene. Alternatively spliced transcript including LTR12C element was detected in the last exon of gene. In order to detect this transcript, we accompanied RT-PCR analysis in the normal and adjacent cancer tissue samples, indicating that this transcript was expressed higher in colorectal cancer than normal tissue samples with similar expression patterns in other cancer tissues (liver, lung, testes). We also confirmed high expression of colorectal cancer in patient sample. The expression level of alternative transcript of CHM gene could be used to predict colorectal cancer. Further study about effect of LTR12C in this alternative transcript between normal and cancer tissues is indicated. Introduction Materials & Methods Lipid envelope Receptor binding proteins Human & Primate genomic DNA RNase 8% Bioinformatics ( in silico analysis CHM gene ) Viral RNA LTR : long terminal repeat LINE : long integrated nuclear element SINE : short integrated nuclear element HERV : Human endogenous retro-virus Genomic DNA PCR & Gene cloning Capsid : core proteins RT PCR ( Human original & EST form) TSD LTR gag pol env PBS gag : coding for matrix and capsid proteins pol : reverse transcriptase and integrase proteins env : product viral envelope and transmembrane structures colorectal tissue samples RT-PCR, Image J analysis Results & Discussion CHM ( choroideremia ) RT-PCR (original transcript & EST form) Chr X M 1 2 3 4 5 6 7 8 9 10 EST q21.2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Original M 11 12 13 14 15 16 17 18 19 20 4 5 EST 85120551 85120427 85105713 85105326 Original CDS UTR MIR/SINE Alu/SINE L1/LINE ERV1/LTR trigger5 M HU CH GO OR GI 1 : adrenal gland, 2 : bone marrow, 3 : adult brain cerebellum, 4 : adult brain whole, 5 : fetal brain, 6 : fetal liver, 7 : heart, 8 : kidney, 9 : liver, 10 : lung, 11 : placenta, 12 : salivary gland, 13 : SK-muscle, 14 : spinal cord, 15 : testis, 16 : prostate, 17 : thymus, 18 : thyroid, 19 : trachea, 20 : uterus Detect LTR12C in primate Transcript including LTR12C RT-PCR (colorectal cancer tissue) N C N C N C Alternative splicing transcript N C N C N C 1 2 3 4 5 N C N C N C N C Reference 1. Gifford R. Tristem M, 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 26(3) : 291-315 2. Mort M. Ivanov D. Cooper DN. Chuzhanova NA, 2008. A meta-analysis of nonsense mutations causing human genetic disease. Hum Mutat. 29(8) : 1037-47