1. Sang-Je Park 1, Kung Ahn 1, Jae-Won Huh 1, Dae-Soo Kim 2, and Heui-Soo Kim 1, 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 Human endogenous retroviruses (HERVs) have been distributed in human genome. HERVs have been considered as etiological cofactors in chronic disease such as cancer, auto immunity, and neurological disease. Among the various HERV families, only HML(human mouse mammary tumor virus-like) group harbor the complete provirus which could amplify their descendant by retrotransposition mechanism. High rate of relationship with cancer development and polymorphic character has been highlighted in biology field. To investigate the expression profiles of HML-4 families, conserved RT(reverse transcriptase) and IN(integrase) domains of pol region were used as target for quantitative real-time RT- PCR analysis. Using the various human and rhesus monkey tissues, HML-4 family was amplified by SYBR green based quantitative real- time RT-PCR. Although, the pol region of HML-4 family was expressed ubiquitously in human and rhesus monkey tissues, SYBR green based quantitative real-time RT-PCR method could be effective technique for the investigation of HERV families. ABSTRACT INTRODUCTION -GENOME INFORMATION LAB.- MATEIRALS & METHODS Structure of HERV-K MA (matrix) protein CA (capsid) protein NC (nucleotide-binding) protein RT (reverse transcriptase) IN (integrase) protein SU (surface) protein TM (transmembrane) protein BioinformaticsPrimer design Sample Preparation Establishment of real-time RT-PCR method for the detection of HML-4 family using SYBR green 0.1 HERV10_1 HERV2 HERV1_3 HERV5_1 HERV5_6 HERV5_5 HERV5_4 HERV5_3 HERV5_2 HERV12_1 HERV12_2 HERVIP10F HERVI HERV11_1 HERV11_2 HERV10_2 HERV7_1 HERV7_2 HERV6 HERVP71A HERV4_2 HERV4_1 HERV4_7 HERV4_6 HERV4_4 HERV4_3 HERV4_5 HERV17 HERV9 HERV30 PABL B GALV PERV BaEV HERVS71 HERVE Harlequin HERV15 HERV3 HERV1_2 HERV1_4 HERV1_1 HERVFH19 HERVH48 HERVH PRIMA4 HERV-P HERVG25 HERV18 HERVL HFV FeFV HERV16 HIV MMTV RERV HERVK3 HERVK22 HERVK11 HERVK11D HERVK13 HERVK9 HERVK14 HERVK10 HERVK14C HERVK4 HERV1 HERV2 HERV4 HERV5 HERV12 HERV11 HERV10 HERV7 HERV6 CLASS Ⅱ CLASS Ⅲ CLASS Ⅰ Gene-related Sequence 36% LINE 20% Other region 16% SINE 13% Coding sequence 3% Pseudogene 1% HERV element 8% DNA element 3% RESULTS & DISCUSSION Measured fluorescence Data analysis Real-time RT-PCR HML4 Rhesus monkey male HML4 Rhesus monkey Female Cerebellum Ccerebrum Heart Lung Salivary gland Testis SK-muscle Trachea Liver Kidney Spleen Stomach Colon Adrenal gland adrenal gland bone marrow cerebellum fetal liver heart liver placenta prostate thymus kidney lung salivary gland testis spinal cord thyroid trachea uterus fetal brain Brain skeletal muscle HML-4 human normal tissues 20 panel colon colon cancer liver uterus cancer breast stomach breast cancer stomach cancer uterus liver cancer HML-4 human normal tissues vs cancer tissues C-33A OVCAR-3 NCI-H250 COLO205 MIA-PaCa-2 Caki-1 RT4 U-937 Hep G2 Jurkat HML-4 cancer cell-line REFERENCES SYBR green based quantitative real-time RT-PCR method could be effective technique for the investigation of HERV families. Cerebellum Ccerebrum Heart Lung Salivary gland Uterus SK-muscle Trachea Liver Kidney Spleen Stomach Colon Adrenal gland Ovary HERVs Leucine (leu) Proline (pro)Alanine (ala)Valine (val) Methionine (met) Tryptophan (trp) Phenylalanine (phe) Isoleucine (ile)Glycine (gly)Serine (ser) Asparagine (asn) Glutamine (gln) Threonine (thr) Cysteine (cys) Tryosine (tyr) Histidine (his) Aspatic acid (asp) Glutamic acid (glu) Lysine (lys) Arginine (arg) LPAVMWFIGSNQTCYHDEKR 1.Rafael Contreras-Galindo, Marta Gonzalez, Sharilyn Almodovar-Camachob, Sandra Gonzalez-Ramirez, Eric Lorenzo, Yasuhiro Yamamura. (2006) A new Real-Time-RT-PCR for quantitation of human endogenous retroviruses type K (HERV-K) RNA load in plasma samples: Increased HERV-K RNA titers in HIV-1 patients with HAART non-suppressive regimens. J Virol Methods. 136(1-2):51-7. 2. Polavarapu N, Bowen NJ, McDonald JF. (2006) Newly identified families of human endogenous retroviruses. J Virol. 80(9):4640-2. 3. Muradrasoli S, Forsman A, Hu L, Blikstad V, Blomberg J. (2006) Development of real-time PCRs for detection and quantitation of human MMTV-like (HML) sequences HML expression in human tissues. J Virol Methods. 136(1-2):83-92. pol U3RU5 RU3 LTR gag env