Expression of alternative transcription including LTR 12 C

Expression of alternative transcription including LTR 12 C in human CHM gene in colorectal cancer Yi-Deun Jung 1, Jae-Won Huh 1, 2, Dae-Soo Kim 3, Hong-Seok Ha 1 and Heui-Soo Kim 1 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 retinaspecific 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 LTR 12 C that are located within the intron 4 of the CHM gene. Alternatively spliced transcript including LTR 12 C 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 LTR 12 C in this alternative transcript between normal and cancer tissues is indicated. Materials & Methods Introduction Lipid Receptor envelope 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) PBS gag LTR TSD pol env LTR colorectal tissue samples RT-PCR, Image J analysis TSD gag : coding for matrix and capsid proteins pol : reverse transcriptase and integrase proteins env : product viral envelope and transmembrane structures Results & Discussion § CHM ( choroideremia ) § RT-PCR (original transcript & EST form) Chr X M 1 2 3 11 12 13 4 5 6 7 8 9 15 16 17 18 19 10 EST q 21. 2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Original M 4 85120551 85105713 20 EST 5 85120427 14 85105326 Original UTR M HU CH CDS MIR/SINE Alu/SINE GO L 1/LINE OR ERV 1/LTR trigger 5 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, § Detect LTR 12 C in primate 15 : testis, 16 : prostate, 17 : thymus, 18 : thyroid, 19 : trachea, 20 : uterus § Transcript including LTR 12 C RT-PCR (colorectal cancer tissue) 3, 5 N C N C 3 2, 5 § Alternative splicing transcript 2 N C N normal cancer 1, 5 C 1 0, 5 1 2 3 4 5 N C N C 0 1 2 3 4 5 6 7 8 9 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