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Comparative and Functional Genomics
Volume 2012 (2012), Article ID 129416, 8 pages
http://dx.doi.org/10.1155/2012/129416
Research Article

High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements

1Department of Nanobiomedical Science & WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea
2Department of Microbiology, College of Advance Science, Dankook University, Cheonan 330-714, Republic of Korea
3Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA

Received 29 July 2011; Revised 25 October 2011; Accepted 31 October 2011

Academic Editor: Brian Wigdahl

Copyright © 2012 Jungnam Lee et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes.