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,
21 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
2 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Koreahttp:// www.primate.or.kr
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.
8%
TSD TSDLTR gag pol env LTR
PBS
gag : coding for matrix and capsid proteinspol : reverse transcriptase and integrase proteins
env : product viral envelope and transmembrane structures
LTR : long terminal repeatLINE : long integrated nuclear elementSINE : short integrated nuclear elementHERV : Human endogenous retro-virus
Human & Primate genomic DNA
Bioinformatics ( in silico analysis ATAD3C gene )
Genomic DNA PCR & Gene cloning
RT PCR ( Human & Rhesus monkey )
Sequencing , Alignment , Image J analysis
1. Nicolas Wentzensen , Johannes F. Coy , Hanns-Peter Knaebel , Michael Linnebacher , Birgit Wilz , Johannes Gebert and Magnus von Knebel Doeberitz , 2007. Expression of an endogenous retroviral sequence from the HERV-H group in gastrointestinal cancers. Int. J. Cancer. 121, 1417-1423.2. 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 , 2006. Trnascriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells . Arch Virol . 151, 1985-1994.
NM_001039211.1
[ ATPase family AAA domain containing 3C ]
p36.33
Chr 1
ATAD3C
Exon 1 2
CDS UTRAluSg/x LTR7BFLAM_CAluSqAluSx
Marker HU CH GO OR GI JM RH NM
616bp
Alu Y
Alu Sx
FLAM_C
LTR 7B
1)2)
1 2
HU
RH
Alu Y
1)
2)
A1
Variant A
Human & Rhesus monkey RT PCR Variant A & A1 1 1-1 2 2-1 3 3-1 4Marker
5 5-1 6 6-1 7 7-1 8Marker
Alu Sq
Alu Sg/x
FLAM_C
Alu Sg/x
LTR7B
New Variant A1
4-1
8-1
8-1
6-1
4-1
2-1
Trachea HU
Lung HU
Kidney HU
Cerebellum HU
Trachea RH8Testis RH7-1Testis HU7
Lung RH6Liver RH5-1Liver HU5
Kidney RH4Heart RH3-1Heart HU3
Cerebellum RH2Adrenal gland RH1-1Adrenal gland HU1
Variant B
Variant B & B1 1 1-1 2 2-1 3 3-1 4 4-1Marker
5 5-1 6 6-1 7 7-1 8 8-1Marker
L1M3
New Variant B1
0
0.5
1
1.5
2
2.5
3
1 1_1 2 2_1 3 3_1 4 4_1 5 5_1 6 6_1 7 7_1 8 8_1
A1 variant B1 variant B variant
[ B variant : 217 bp , B1 variant : 326 bp ]
B
B1
B
B1
[ A variant : 1482 bp , A1 variant : 798 bp ]
RT PCR Image analysis
RNase
Viral RNA
Capsid : core proteins
Receptor
binding
proteins
Lipid
envelope
A1