Genome-wide analysis of the human <it>Alu </it>Yb-lineage
<p>Abstract</p> <p>The <it>Alu </it>Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2004-03-01
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| Series: | Human Genomics |
| Subjects: | |
| Online Access: | http://www.humgenomics.com/content/1/3/167 |
| _version_ | 1798006386985009152 |
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| author | Carter Anthony B Salem Abdel-Halim Hedges Dale J Keegan Catherine Kimball Beth Walker Jerilyn A Watkins W Jorde Lynn B Batzer Mark A |
| author_facet | Carter Anthony B Salem Abdel-Halim Hedges Dale J Keegan Catherine Kimball Beth Walker Jerilyn A Watkins W Jorde Lynn B Batzer Mark A |
| author_sort | Carter Anthony B |
| collection | DOAJ |
| description | <p>Abstract</p> <p>The <it>Alu </it>Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for <it>Alu </it>Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb <it>Alu </it>subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the <it>Alu </it>Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage <it>Alu </it>elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx <it>Alu </it>family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that <it>Alu </it>Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the <it>Alu </it>Yb elements will be useful in a wide range of genetic analyses.</p> |
| first_indexed | 2024-04-11T12:55:07Z |
| format | Article |
| id | doaj.art-556a6200d3904b599b2980128c4817f5 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-11T12:55:07Z |
| publishDate | 2004-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-556a6200d3904b599b2980128c4817f52022-12-22T04:23:06ZengBMCHuman Genomics1479-73642004-03-011316717810.1186/1479-7364-1-3-167Genome-wide analysis of the human <it>Alu </it>Yb-lineageCarter Anthony BSalem Abdel-HalimHedges Dale JKeegan CatherineKimball BethWalker Jerilyn AWatkins WJorde Lynn BBatzer Mark A<p>Abstract</p> <p>The <it>Alu </it>Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for <it>Alu </it>Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb <it>Alu </it>subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the <it>Alu </it>Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage <it>Alu </it>elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx <it>Alu </it>family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that <it>Alu </it>Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the <it>Alu </it>Yb elements will be useful in a wide range of genetic analyses.</p>http://www.humgenomics.com/content/1/3/167mobile elementsSINEs |
| spellingShingle | Carter Anthony B Salem Abdel-Halim Hedges Dale J Keegan Catherine Kimball Beth Walker Jerilyn A Watkins W Jorde Lynn B Batzer Mark A Genome-wide analysis of the human <it>Alu </it>Yb-lineage Human Genomics mobile elements SINEs |
| title | Genome-wide analysis of the human <it>Alu </it>Yb-lineage |
| title_full | Genome-wide analysis of the human <it>Alu </it>Yb-lineage |
| title_fullStr | Genome-wide analysis of the human <it>Alu </it>Yb-lineage |
| title_full_unstemmed | Genome-wide analysis of the human <it>Alu </it>Yb-lineage |
| title_short | Genome-wide analysis of the human <it>Alu </it>Yb-lineage |
| title_sort | genome wide analysis of the human it alu it yb lineage |
| topic | mobile elements SINEs |
| url | http://www.humgenomics.com/content/1/3/167 |
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