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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 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 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.
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
q21.2
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
L1/LINE
OR
ERV1/LTR
trigger5
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 LTR12C
in primate
15 : testis, 16 : prostate, 17 : thymus, 18 : thyroid, 19 : trachea, 20 : uterus
 Transcript including LTR12C RT-PCR (colorectal cancer tissue)
N
C
N
C
N
C
3.5
3
 Alternative splicing transcript
2.5
N
C
N
C
N
C
2
normal
cancer
1.5
1
1
2
3 4
5
N
C
N
C
N
C
N
C
0.5
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