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High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
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 bi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286893/ https://www.ncbi.nlm.nih.gov/pubmed/22400009 http://dx.doi.org/10.1155/2012/129416 |
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author | Lee, Jungnam Mun, Seyoung Meyer, Thomas J. Han, Kyudong |
author_facet | Lee, Jungnam Mun, Seyoung Meyer, Thomas J. Han, Kyudong |
author_sort | Lee, Jungnam |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3286893 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-32868932012-03-07 High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements Lee, Jungnam Mun, Seyoung Meyer, Thomas J. Han, Kyudong Comp Funct Genomics Research Article 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. Hindawi Publishing Corporation 2012 2012-02-07 /pmc/articles/PMC3286893/ /pubmed/22400009 http://dx.doi.org/10.1155/2012/129416 Text en Copyright © 2012 Jungnam Lee et al. https://creativecommons.org/licenses/by/3.0/ 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. |
spellingShingle | Research Article Lee, Jungnam Mun, Seyoung Meyer, Thomas J. Han, Kyudong High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title | High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title_full | High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title_fullStr | High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title_full_unstemmed | High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title_short | High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements |
title_sort | high levels of sequence diversity in the 5′ utrs of human-specific l1 elements |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286893/ https://www.ncbi.nlm.nih.gov/pubmed/22400009 http://dx.doi.org/10.1155/2012/129416 |
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