Genome Information Lab

1. LTR ORF1 ORF2 LTR Yeast Ty1/copia/truncated HERVs LTR LTR Human THE1 LTR gag pol env LTR Full-length HERVs/exogenous retrovirus PNU PNU Abstract Results & Discussion M HU CH GO GI JM RM 641 b p SINE HU GO I BO GI OR CR CA JM SQ II RH TA NM MAN LAN COL 0.025 0.020 0.015 0.010 0.005 0.000 PNU Materials & Methods Gene Cloning & Sequencing PCR Bioinformatics Template DNA 94℃ Denature 50℃ Anneal Primer 72℃ PNU DNA polymerase X 35 Extension References Evolutionary relationship of LIPH gene and Alu element Jin-Han Bae1, Sang-Je Park1, 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, Republicof Korea http:// www.primate.or.kr LIPH gene (Lipase member H) located on human 3q27 is reported to be related to hair growth and loss by deletion mechanism of fourth exon. The deletion mechanism is occurred by the homologous recombination and excision event of similar Alu elements of AluSc and AluY. In this report, we investigated the evolutionary mechanism and conservation of exon 4 sequences of LIPH gene. PCR amplification indicated that AluY element have been integrated into our common ancestor genome after the divergence of Old World monkeys and Hominoid primate. Sequencing analysis of various primates DNA samples (5 hominoids, 6 Old World monkeys, and 4 New World monkeys) of exon 4 region shows one non-synonymous substitution, indicating that the region is important portion for the functional protein. The substitution event from Iso to Thr has been occurred in hominoid lineage.………………………………….………… L I P H (lipase, member H) Chr.3 Exon 1 2 3 4 5 6 7 8 9 10 S … AS 3q27 AluSc AluY MIR CDS UTR Insertion of AluY Sequence analysis of Exon4 in LIPH Sequence analysis of AluY PNU Introduction Retroelement Pseudogene Gene-related Sequence RNA intermediate 1% Coding sequence 36% 3% - LTR element + LTR element DNA element Amino acids of Exon4 in LIPH Phylogenic analysis of Exon4 in LIPH 3% Retroposon HERV element - env + env 8% Retrotrnasposon - RT + RT P LINE Poly(A) 20% Human Alu Other region Retrovirus SINE 16% LINE 13% P ORF1 ORF2 Poly(A) L1 7SL-derived left A-rich 7SL-derived right poly(A) monomer connector monomer TSD TSD Sequence analysis of Exon4 in various species A box B box Hu Ch Canis Mus Gallus Rabbit Frog Hu Ch Canis Mus Gallus Rabbit Frog Hu Ch Canis Mus Gallus Rabbit Frog Hu Ch Canis Mus Gallus Rabbit Frog Hu Ch Canis Mus Gallus Rabbit Frog • Kazantseva A, Goltsov A, Zinchenko R, Grigorenko AP, Abrukova AV, Moliaka YK, Kirillov AG, Guo Z, Lyle S, Ginter EK, Rogaev EI. Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH. Science. 2006 Nov 10;314(5801):982-5. • 2. Ali G, Chishti MS, Raza SI, John P, Ahmad W. A mutation in the lipase H (LIPH) gene underlie autosomal recessive hypotrichosis. Hum Genet. 2007 May;121(3-4):319-25. Epub 2007 Feb 27. • 3. Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet. 2007 Apr;23(4):183-91. Epub 2007 Feb 27. Review. Genome Information Lab http:// www.primate.or.kr