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