Detection of alternative transcripts including HERV-H LTR of the human ATAD3C gene

1. Alu Sg/x FLAM_C FLAM_C Alu Sg/x LTR 7B LTR7B Alu Y Alu Sq Alu Sx 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. PBS TSD LTR gag pol env LTR TSD gag : coding for matrix and capsid proteins pol : reverse transcriptase and integrase proteins env : product viral envelope and transmembrane structures 616bp 1 Adrenal gland HU 1-1 Adrenal gland RH 2 Cerebellum HU 2-1 Cerebellum RH 3 Heart HU 3-1 Heart RH 4 Kidney HU 4-1 Kidney RH 5 Liver HU 5-1 Liver RH 6 Lung HU 6-1 Lung RH 7 Testis HU 7-1 Testis RH 8 Trachea HU 8-1 Trachea RH RH 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 Lipid envelope Receptor binding proteins Human & Primate genomic DNA RNase 8% Bioinformatics ( in silico analysis ATAD3C gene ) Viral RNA Genomic DNA PCR & Gene cloning LTR : long terminal repeat LINE : long integrated nuclear element SINE : short integrated nuclear element HERV : Human endogenous retro-virus Capsid : core proteins RT PCR ( Human & Rhesus monkey ) Sequencing , Alignment , Image J analysis ATAD3C [ ATPase family AAA domain containing 3C ] Variant A Variant B Chr 1 New Variant A1 New Variant B1 p36.33 NM_001039211.1 Exon 1 2 • Human & Rhesus monkey RT PCR • Variant B & B1 • Variant A & A1 [ A variant : 1482 bp , A1 variant : 798 bp ] [ B variant : 217 bp , B1 variant : 326 bp ] AluSg/x LTR7B CDS UTR AluSx AluSq FLAM_C Marker 1 1-1 2 2-1 3 3-1 4 4-1 Marker 1 1-1 2 2-1 3 3-1 4 4-1 Marker HU CH GO OR GI JM RH NM 2) 1) B1 A1 B Marker 5 5-1 6 6-1 7 7-1 8 8-1 8-1 Marker 5 5-1 6 6-1 7 7-1 8 B1 A1 B L1M3 • RT PCR Image analysis 1 2 HU 1) 2) 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.