<it>Alu</it> expression in human cell lines and their retrotranspositional potential
<p><b>Abstract</b></p> <p><b>Background</b></p> <p>The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as ‘source elements’ can generate new Alu insertions. The first step in id...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-06-01
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| Series: | Mobile DNA |
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| Online Access: | http://www.mobilednajournal.com/content/3/1/11 |
| _version_ | 1818346808545378304 |
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| author | Oler Andrew J Traina-Dorge Stephen Derbes Rebecca S Canella Donatella Cairns Brad R Roy-Engel Astrid M |
| author_facet | Oler Andrew J Traina-Dorge Stephen Derbes Rebecca S Canella Donatella Cairns Brad R Roy-Engel Astrid M |
| author_sort | Oler Andrew J |
| collection | DOAJ |
| description | <p><b>Abstract</b></p> <p><b>Background</b></p> <p>The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as ‘source elements’ can generate new Alu insertions. The first step in identifying the active Alu sources is to determine the loci transcribed by RNA polymerase III (pol III). Previous genome-wide analyses from normal and transformed cell lines identified multiple Alu loci occupied by pol III factors, making them candidate source elements.</p> <p><b>Findings</b></p> <p>Analysis of the data from these genome-wide studies determined that the majority of pol III-bound Alus belonged to the older subfamilies Alu S and Alu J, which varied between cell lines from 62.5% to 98.7% of the identified loci. The pol III-bound Alus were further scored for estimated retrotransposition potential (ERP) based on the absence or presence of selected sequence features associated with Alu retrotransposition capability. Our analyses indicate that most of the pol III-bound Alu loci candidates identified lack the sequence characteristics important for retrotransposition.</p> <p><b>Conclusions</b></p> <p>These data suggest that Alu expression likely varies by cell type, growth conditions and transformation state. This variation could extend to where the same cell lines in different laboratories present different Alu expression patterns. The vast majority of Alu loci potentially transcribed by RNA pol III lack important sequence features for retrotransposition and the majority of potentially active Alu loci in the genome (scored high ERP) belong to young Alu subfamilies. Our observations suggest that in an <it>in vivo</it> scenario, the contribution of Alu activity on somatic genetic damage may significantly vary between individuals and tissues.</p> |
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| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-13T17:24:09Z |
| publishDate | 2012-06-01 |
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| series | Mobile DNA |
| spelling | doaj.art-e3b5f4dc083349728faa0ddd235446ea2022-12-21T23:37:14ZengBMCMobile DNA1759-87532012-06-01311110.1186/1759-8753-3-11<it>Alu</it> expression in human cell lines and their retrotranspositional potentialOler Andrew JTraina-Dorge StephenDerbes Rebecca SCanella DonatellaCairns Brad RRoy-Engel Astrid M<p><b>Abstract</b></p> <p><b>Background</b></p> <p>The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as ‘source elements’ can generate new Alu insertions. The first step in identifying the active Alu sources is to determine the loci transcribed by RNA polymerase III (pol III). Previous genome-wide analyses from normal and transformed cell lines identified multiple Alu loci occupied by pol III factors, making them candidate source elements.</p> <p><b>Findings</b></p> <p>Analysis of the data from these genome-wide studies determined that the majority of pol III-bound Alus belonged to the older subfamilies Alu S and Alu J, which varied between cell lines from 62.5% to 98.7% of the identified loci. The pol III-bound Alus were further scored for estimated retrotransposition potential (ERP) based on the absence or presence of selected sequence features associated with Alu retrotransposition capability. Our analyses indicate that most of the pol III-bound Alu loci candidates identified lack the sequence characteristics important for retrotransposition.</p> <p><b>Conclusions</b></p> <p>These data suggest that Alu expression likely varies by cell type, growth conditions and transformation state. This variation could extend to where the same cell lines in different laboratories present different Alu expression patterns. The vast majority of Alu loci potentially transcribed by RNA pol III lack important sequence features for retrotransposition and the majority of potentially active Alu loci in the genome (scored high ERP) belong to young Alu subfamilies. Our observations suggest that in an <it>in vivo</it> scenario, the contribution of Alu activity on somatic genetic damage may significantly vary between individuals and tissues.</p>http://www.mobilednajournal.com/content/3/1/11Alu source elementsAlu expressionRT-PCRChIP-seqRetrotranspositionSINE |
| spellingShingle | Oler Andrew J Traina-Dorge Stephen Derbes Rebecca S Canella Donatella Cairns Brad R Roy-Engel Astrid M <it>Alu</it> expression in human cell lines and their retrotranspositional potential Mobile DNA Alu source elements Alu expression RT-PCR ChIP-seq Retrotransposition SINE |
| title | <it>Alu</it> expression in human cell lines and their retrotranspositional potential |
| title_full | <it>Alu</it> expression in human cell lines and their retrotranspositional potential |
| title_fullStr | <it>Alu</it> expression in human cell lines and their retrotranspositional potential |
| title_full_unstemmed | <it>Alu</it> expression in human cell lines and their retrotranspositional potential |
| title_short | <it>Alu</it> expression in human cell lines and their retrotranspositional potential |
| title_sort | it alu it expression in human cell lines and their retrotranspositional potential |
| topic | Alu source elements Alu expression RT-PCR ChIP-seq Retrotransposition SINE |
| url | http://www.mobilednajournal.com/content/3/1/11 |
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