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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...

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Autores principales: Warburton, Peter E, Hasson, Dan, Guillem, Flavia, Lescale, Chloe, Jin, Xiaoping, Abrusan, Gyorgy
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
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.
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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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