• Genomics & Informatics
• /
• v.10 no.4
• /
• pp.226-233
• /
• 2012

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

• Clinical and Experimental Reproductive Medicine
• /
• v.43 no.2
• /
• pp.82-89
• /
• 2016

Objective: The long interspersed elements (LINE-1, L1s) are a group of genetic elements found in large numbers in the human genome that can translate into phenotype by controlling genes. Growing evidence supports the role of epigenetic in polycystic ovary syndrome (PCOS). The purpose of this study is to evaluate the DNA methylation levels in LINE-1 in a tissue-specific manner using cumulus cells from patients with PCOS compared with normal controls. Methods: The study included 19 patients with PCOS and 22 control patients who were undergoing controlled ovarian hyperstimulation. After oocyte retrieval, cumulus cells were extracted. LINE-1 DNA methylation levels were analysed by bisulfite treatment, polymerase chain reaction, and restriction enzyme digestion. The Connection Up- and Down-Regulation Expression Analysis of Microarrays software package was used to compare the gene regulatory functions of intragenic LINE-1. Results: The results showed higher LINE-1 DNA methylation levels in the cumulus cells of mature oocytes in PCOS patients, 79.14 (${\pm}2.66$) vs. 75.40 (${\pm}4.92$); p=0.004, but no difference in the methylation of cumulus cells in immature oocytes between PCOS and control patients, 70.33 (${\pm}4.79$) vs. 67.79 (${\pm}5.17$); p=0.155. However, LINE-1 DNA methylation levels were found to be higher in the cumulus cells of mature oocytes than in those of immature oocytes in both PCOS and control patients. Conclusion: These findings suggest that the epigenetic modification of LINE-1 DNA may play a role in regulating multiple gene expression that affects the pathophysiology and development of mature oocytes in PCOS.

• Journal of Marine Bioscience and Biotechnology
• /
• v.1 no.3
• /
• pp.186-192
• /
• 2006

Short interspersed repetitive elements (SINEs) are dispersed throughout eukaryotic genomes. These SINEs have been shown to be excellent phylogenetic markers for the closed related species. In this report, we isolated two novel families of SINEs from the mud loach. The two SINE families, mlSINE-L and mlSINE-S, have genomic lengths of about 410bp and 270bp, respectively. 5' and 3' ends of the SINE families are well conserved and highly homologous to each of corresponding ends of RSg-1 and SmaI SINEs. Phylogenetic analysis shows that mlSINEs are unique to the mud loach. A dot blot hybridization experiment shows that mlSINE-L has an estimated copy number of $1{\times}10^3$ per $2{\times}10^9bp$ (2.8 pg) and is more frequently distributed at nuclear matrix attachment regions (MARs) than loop DNAs. The result suggests that mlSINEs may preferentially integrate in or near MARs.