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 609-735, Republic of Korea 2 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea http:// 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. 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_001039211.1 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 , 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. Genome Information Lab.