Analysis of the largest tandemly repeated DNA families in the human genome.
Analysis of the largest tandemly repeated DNA families in the human genome.
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分析人类基因组中最大的串联重复DNA家族。
DOI：
10.1186/1471-2164-9-533
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发表时间：
2008-11-07
期刊：
影响因子：
4.4
通讯作者：
Abrusan, Gyorgy
中科院分区：
文献类型：
--
作者：
Warburton, Peter E.;Hasson, Dan;Guillem, Flavia;Lescale, Chloe;Jin, Xiaoping;Abrusan, Gyorgy
串联重复DNA代表了人类基因组的很大一部分，并解释了大量的拷贝数变异。在这里，我们提出了在人类基因组序列中发现的最大串联重复的全基因组分析。使用串联重复序列分析（TRF），鉴定总大小大于10 kb的串联重复序列阵列，并将其分为简单序列（例如GAATG）、经典卫星（例如α卫星DNA）和基因座特异性VNTR阵列。这些大的测序区域的分析表明，几个“简单序列”阵列实际上显示复杂的结构域和/或更高阶的重复组织。使用额外的方法，我们进一步确定了总共96个额外的阵列与串联重复单位大于2 kb（TRF的检测限），其中53个包含基因或重复外显子。发现跨越8号染色体上的间隙的串联12 kb重复序列的阵列的总体大小为600 kb至1.7 Mbp，代表表征的最大的非着丝粒阵列之一。观察到几个新的巨卫星串联DNA家族，其特征在于散布的转座因子的重复模式，这些转座因子可能通过不等交换而扩展。其中一个家族在11条不同的染色体上发现，超过25个阵列，代表了最大最广泛的巨卫星DNA家族之一。这项研究代表了人类基因组中大串联重复序列的最全面的全基因组分析，并将作为了解这些复杂DNA家族的组织和拷贝数变异的重要资源。
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. 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. 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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