1. Detection of alternative transcripts including HERV-H LTR of the human ATAD3C gene
Yi-Deun Jung1, Jae-Won Huh1, Dae-Soo Kim2 and Heui-Soo Kim1, 2
1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan , Republic of Korea
2 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan , Republic of Korea
ATAD3C (ATPase family AAA domain containing 3C) gene located on human chromosome 1p36.33 has activity of coenzyme and enzyme regulator. GenBank database searching indicates the two different alternative transcript of ATAD3C (variant A and variant B). Variant A is revealed to be related with HERV-H LTR which has been integrated into our common ancestor genome between Old World monkeys and New World monkeys. RT-PCR analysis shows that variant A is expressed specifically in lung tissue. We identified variant A1 transcript which is expressed ubiquitously in human and rhesus monkey tissues. In the case of transcript B, both of human and rhesus monkey tissues show similar expression patterns. RT-PCR analysis of transcript B indicated that alternatively spliced transcript of transcript B1 related to L1M3 element was identified. These findings suggest that the integration event of H-LTR element in ATAD3C gene could be resources for the diversification of gene transcripts during the primate evolution.
Lipid
envelope
Receptor
binding
proteins
Human & Primate genomic DNA
RNase 8%
Bioinformatics ( in silico analysis ATAD3C 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 & Rhesus monkey )
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
Sequencing , Alignment , Image J analysis
ATAD3C
[ ATPase family AAA domain containing 3C ]
Variant A
Variant B
Chr 1
p36.33
New Variant A1
New Variant B1
NM_
Exon 1 2
Human & Rhesus monkey RT PCR
Variant A & A1
Variant B & B1
AluSx
AluSq
AluSg/x
FLAM_C
LTR7B
CDS
UTR
[ A variant : 1482 bp , A1 variant : 798 bp ]
[ B variant : 217 bp , B1 variant : 326 bp ]
Marker 1
1-1 2
2-1 3
3-1 4
4-1
Marker 1
1-1 2
2-1 3
3-1 4
Marker HU CH GO OR GI JM RH NM
4-1 2)
616bp 1) B1 A1 B
Alu Y
Alu Sx
FLAM_C
Marker 5
5-1 6
6-1 7
7-1 8
8-1
Marker 5
5-1 6
6-1 7
7-1 8
8-1 B1 A1 B
Alu Sq
L1M3
RT PCR Image analysis
LTR 7B
Alu Sg/x
FLAM_C
LTR7B 1 2
8-1
6-1
4-1
2-1
Trachea HU
Lung HU
Kidney HU
Cerebellum HU
Trachea RH 8
Testis RH
7-1
Testis HU 7
Lung RH 6
Liver RH
5-1
Liver HU 5
Kidney RH 4
Heart RH
3-1
Heart HU 3
Cerebellum RH 2
Adrenal gland RH
1-1
Adrenal gland HU 1 1) HU 2) RH
Alu Y
1. Nicolas Wentzensen , Johannes F. Coy , Hanns-Peter Knaebel , Michael Linnebacher , Birgit Wilz , Johannes Gebert and Magnus von Knebel Doeberitz , Expression of an endogenous retroviral sequence from the HERV-H group in gastrointestinal cancers. Int. J. Cancer. 121,
2. H.-S.Sin , J.-W.Huh , D.-S.Kim , D.W.Kang , D.S.Min , T.-H.Kim , H.-S.Ha , H.-H.Kim , S.-Y.Lee , and H.-S.Kim , Trnascriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells . Arch Virol . 151,
Genome Information Lab.