1. 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 , 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
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
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, The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 26(3) :
2. Mort M. Ivanov D. Cooper DN. Chuzhanova NA, A meta-analysis of nonsense mutations causing human genetic disease. Hum Mutat. 29(8) :