1. ALTERNATIVE TRANSCIPTION OF HUMAN
CHM GENE INCLUDING LTR12C ELEMENT IN COLORECTAL CANCER
Yi-Deun Jung1, Yun-Ji Kim1, Jae-Won Huh2, Dae-Soo Kim3, Hong-Seok Ha1, Eun-Sang Choi1,
Won-Ho Lee1 and Heui-Soo Kim1
1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan , Republic of Korea
2 National Primate Research Center, KRIBB, Ochang, Chungbuk , Republic of Korea
3 Korea Bioinformation Center, KRIBB, Daejeon , Republic of Korea
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
Human & Primate genomic DNA
RNase
Viral RNA
Capsid : core proteins
Receptor
binding
proteins
Lipid
envelope
Bioinformatics ( in silico analysis CHM gene ) 8%
Genomic DNA PCR & Gene Cloning
LTR : long terminal repeat
LINE : long integrated nuclear element
SINE : short integrated nuclear element
HERV : Human endogenous retro-virus
RT PCR ( Human original & EST form)
colorectal tissue samples RT-PCR, Image J analysis
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
Results & Discussion
CHM ( choroideremia )
Analyzed quantitatively using the Image-J program
Chr X
q21.2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 4 5
RT-PCR (original transcript & EST form)
CDS
UTR
MIR/SINE
Alu/SINE
L1/LINE
ERV1/LTR
trigger5 M 1 2 3 4 5 6 7 8 9 10
Alternative splicing transcript
EST
Original 1 2 3 4 5 M 11 12 13 14 15 16 17 18 19 20
Transcript including LTR12C RT-PCR (colorectal cancer tissue)
EST
Original N C N C N C N C N C N C
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 N C N C N C N C
References
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Scheef G, Fischer N, Krach U, Tonjes RR (2001) The number of a U3 repeat box acting as an enhancer in long terminal repeats of polytropic
replication-competent porcine endogenous retroviruses dynamically fluctuates during serial virus passages in human cells. J Virol 75: