Identification and phylogeny of the human endogenous retrovirus HERV-W LTR family in cancer cells

Abstract

The long terminal repeats (LTRs ) of human endogenous retrovirus (HERV) have been found to be coexpressed with sequences of closely located genes. It has been suggested that the LTR elements have contributed to the structural change or genetic variation of human genome connected to various diseases and evolution. We examined the HERV-W LTR elements in various cancer cells (2F7, A43 1, A549, HepG2 , MIA-PaCa-2 , PC-3, RT4 , SiHa, U-937, and UO-3 1). Using genomic DNA from the cancer cells , we performed PCR amplific ation and identified twelve new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (88-99%) with HERV-W LTR (AF072500). A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-W LTR elements could be mainly divided into two groups through evolutionary divergence. Three HERV-W LTR elements (RT4-2 , A43 1-1, and UO3 1-2) belonged to Group I, where as nine LTR elements (2F7-2 , A549-1, A549-3, HepG2-3, MP2-2 , PC3-1, SiHa-8, SiHa-10, and U937-1) belonged to Group II. Taken together, our new sequence data of the HERV-W LTR elements may contribute to an understanding of tissue-specific cancer by genomic instability of LTR integration.