Alu elements in primates are preferentially lost from areas of high GC content
The currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Alt...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2013-05-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/78.pdf |
| _version_ | 1797419790500888576 |
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| author | Elizabeth HB Hellen John FY Brookfield |
| author_facet | Elizabeth HB Hellen John FY Brookfield |
| author_sort | Elizabeth HB Hellen |
| collection | DOAJ |
| description | The currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of studies have tackled the problem, no analysis has definitively explained the reason for this trend. These observations have been made by relying on the subfamily as a proxy for age of an element. In this study, we suggest that this is a misleading assumption and instead analyse the relationship between the taxonomic distribution of an individual element and its surrounding GC environment. An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. We show that the previously-reported effect of GC content correlating with subfamily age is not reflected by the ages of the individual elements. Instead, elements are preferentially lost from areas of high GC content over time. The correlation between GC content and subfamily may be due to a change in insertion bias in the young subfamilies. The link between Alu subfamily age and GC region was made due to an over-simplification of the data and is incorrect. We suggest that use of subfamilies as a proxy for age is inappropriate and that the analysis of ortholog presence in other primate species provides a deeper insight into the data. |
| first_indexed | 2024-03-09T06:52:17Z |
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| id | doaj.art-9d3157aecff64ca0a5aa3e9f9bb72f21 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:52:17Z |
| publishDate | 2013-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-9d3157aecff64ca0a5aa3e9f9bb72f212023-12-03T10:22:41ZengPeerJ Inc.PeerJ2167-83592013-05-011e7810.7717/peerj.7878Alu elements in primates are preferentially lost from areas of high GC contentElizabeth HB Hellen0John FY Brookfield1Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, UKCentre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, UKThe currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of studies have tackled the problem, no analysis has definitively explained the reason for this trend. These observations have been made by relying on the subfamily as a proxy for age of an element. In this study, we suggest that this is a misleading assumption and instead analyse the relationship between the taxonomic distribution of an individual element and its surrounding GC environment. An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. We show that the previously-reported effect of GC content correlating with subfamily age is not reflected by the ages of the individual elements. Instead, elements are preferentially lost from areas of high GC content over time. The correlation between GC content and subfamily may be due to a change in insertion bias in the young subfamilies. The link between Alu subfamily age and GC region was made due to an over-simplification of the data and is incorrect. We suggest that use of subfamilies as a proxy for age is inappropriate and that the analysis of ortholog presence in other primate species provides a deeper insight into the data.https://peerj.com/articles/78.pdfTransposonsAluYoungOldGC contentInsertion bias |
| spellingShingle | Elizabeth HB Hellen John FY Brookfield Alu elements in primates are preferentially lost from areas of high GC content PeerJ Transposons Alu Young Old GC content Insertion bias |
| title | Alu elements in primates are preferentially lost from areas of high GC content |
| title_full | Alu elements in primates are preferentially lost from areas of high GC content |
| title_fullStr | Alu elements in primates are preferentially lost from areas of high GC content |
| title_full_unstemmed | Alu elements in primates are preferentially lost from areas of high GC content |
| title_short | Alu elements in primates are preferentially lost from areas of high GC content |
| title_sort | alu elements in primates are preferentially lost from areas of high gc content |
| topic | Transposons Alu Young Old GC content Insertion bias |
| url | https://peerj.com/articles/78.pdf |
| work_keys_str_mv | AT elizabethhbhellen aluelementsinprimatesarepreferentiallylostfromareasofhighgccontent AT johnfybrookfield aluelementsinprimatesarepreferentiallylostfromareasofhighgccontent |