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Analysis of the largest tandemly repeated DNA families in the human genome
BACKGROUND: Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. RESULTS: Using Tandem Repeats Finder (TRF), tande...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588610/ https://www.ncbi.nlm.nih.gov/pubmed/18992157 http://dx.doi.org/10.1186/1471-2164-9-533 |
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author | Warburton, Peter E Hasson, Dan Guillem, Flavia Lescale, Chloe Jin, Xiaoping Abrusan, Gyorgy |
author_facet | Warburton, Peter E Hasson, Dan Guillem, Flavia Lescale, Chloe Jin, Xiaoping Abrusan, Gyorgy |
author_sort | Warburton, Peter E |
collection | PubMed |
description | BACKGROUND: Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. RESULTS: Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. CONCLUSION: This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families. |
format | Text |
id | pubmed-2588610 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25886102008-11-28 Analysis of the largest tandemly repeated DNA families in the human genome Warburton, Peter E Hasson, Dan Guillem, Flavia Lescale, Chloe Jin, Xiaoping Abrusan, Gyorgy BMC Genomics Research Article BACKGROUND: Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. RESULTS: Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. CONCLUSION: This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families. BioMed Central 2008-11-07 /pmc/articles/PMC2588610/ /pubmed/18992157 http://dx.doi.org/10.1186/1471-2164-9-533 Text en Copyright © 2008 Warburton et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Warburton, Peter E Hasson, Dan Guillem, Flavia Lescale, Chloe Jin, Xiaoping Abrusan, Gyorgy Analysis of the largest tandemly repeated DNA families in the human genome |
title | Analysis of the largest tandemly repeated DNA families in the human genome |
title_full | Analysis of the largest tandemly repeated DNA families in the human genome |
title_fullStr | Analysis of the largest tandemly repeated DNA families in the human genome |
title_full_unstemmed | Analysis of the largest tandemly repeated DNA families in the human genome |
title_short | Analysis of the largest tandemly repeated DNA families in the human genome |
title_sort | analysis of the largest tandemly repeated dna families in the human genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588610/ https://www.ncbi.nlm.nih.gov/pubmed/18992157 http://dx.doi.org/10.1186/1471-2164-9-533 |
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