Identification and phylogeny of new human endogenous retroviral sequences belonging to the HERV-H family

DNA hypomethylation and human diseases

Changes in human DNA methylation patterns are an important feature of cancer development and progression and a potential role in other conditions such as atherosclerosis and autoimmune diseases (e.g., multiple sclerosis and lupus) is being recognised. The cancer genome is frequently characterised by hypermethylation of specific genes concurrently with an overall decrease in the level of 5 methyl cytosine. This hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and is believed to result in chromosomal instability and increased mutation events. This review examines our understanding of the patterns of cancer-associated hypomethylation, and how recent advances in understanding of chromatin biology may help elucidate the mechanisms underlying repeat sequence demethylation. It also considers how global demethylation of repeat sequences including transposable elements and the site-specific hypomethylation of certain genes might contribute to the deleterious effects that ultimately result in the initiation and progression of cancer and other diseases. The use of hypomethylation of interspersed repeat sequences and genes as potential biomarkers in the early detection of tumors and their prognostic use in monitoring disease progression are also examined.

Molecular evolution of the HERV-E family in primates

More than 50 copies of HERV-E family elements have been estimated to exist in the human genome. Here we examined the recent evolutionary history of the HERV-E family by a PCR approach using genomic DNA from hominoid primates and a human monochromosomal panel. From the HERV-E family, 25 and 68 env fragments, were identified and analyzed from hominoid primates and human chromosomes 1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19, X, and Y, respectively. They showed 76.7-99.6% sequence similarity to that of HERV-E (accession no. M10976). Phylogenetic analysis of HERV-E env family distinctively divided into two groups (groups I and II) that each contained three subgroups. Divergence times of the two groups were estimated as 10.7 MYr for group I and 41.3 MYr for group II using an average evolutionary rate of 0.3% per MYr. These data are consistent with that of PCR analysis, which showed a band of the HERV-E family in the genomes of the hominoids, Old World monkeys, and New World monkeys. Therefore, the HERV-E family may have integrated into the primate genome after prosimians and New World monkeys diverged. Then they proliferated extensively in the genome of humans and great apes during primate evolution.

Expression analysis of endogenous retroviral elements belonging to the HERV-F family from human tissues and cancer cells

Based on the primer binding site for Phe-tRNA, human endogenous retroviruses (HERVs) have been classified as HERV-F family members, HERV-F, HERV-FXA, HERV-Fb, and HERV-Fc. The HERV-F family was expressed in human placenta preferentially. We investigated pol fragments of HERV-F family in various human tissues and cancer cells. The pol gene was expressed in human placenta only among tissues (brain, prostate, testis, heart, kidney, liver, lung, placenta, skeletal muscle, spleen, thymus, uterus), but detected in various cancer cell lines (RT4, BT-474, HCT-116, TE-1, UO-31, Jurkat, A549, MCF7, OVCAR-3, MIA-PaCa-2, PC3, LOX-IMVI, AZ521, 2F7, U-937, and C-33A) except for PFSK-1 and HepG2 by RT-PCR analysis. Expression and sequencing data of the 37 clones imply that the pol gene of HERV-F family is active in cancer cells, which may have potential role related to cancer development.

Evolutionary implication of human endogenous retrovirus HERV-H family

The human endogenous retrovirus (HERV-H) family is most abundant and widely distributed in the human genome, with about 100-1,000 full-length or deleted elements and a similar number of solitary, long-terminal repeats. The HERV-H env ORF has been characterized in humans and in the course of primate evolution, indicating the increased possibility of biological roles in humans. Using the polymerase chain reaction approach with a human monochromosomal DNA panel, 70 env fragments belonging to the HERV-H family from chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, X, and Y were identified and analyzed. They showed 82-99% sequence similarity to that of HERV-H (accession no. AF108843). We also identified other HERV-H env fragments in the DDBJ/EMBL/GenBank databases. The total of 120 fragments was evolutionarily analyzed. Phylogenetic analysis suggests that the HERV-H env family is divided into one major and two minor groups. The HERV-H members have been actively proliferated and evolved by intra-chromosomal spread during hominid radiation.