Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes
Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes
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DOI：
10.1101/gr.2542904
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发表时间：
2004-10-01
期刊：
影响因子：
7
通讯作者：
Benson, G
中科院分区：
文献类型：
--
作者：
Warburton, PE;Giordano, J;Benson, G
我们已经进行了第一次全基因组分析的反向重复序列（IR）结构在人类基因组中，使用一种新颖而有效的软件包称为反向重复序列（IRF）。在掩蔽已知重复元件后，IRF检测到22，624个人IR，其特征在于臂大小为25 bp至>100 kb，具有至少75%的同一性，间隔区长度LIP至100 kb。该分析需要在台式PC上进行6小时。总共有166个IR的臂长>8 kb。从这个集合中，如果IR是基因组中未完成/未组装的区域，或者与其他密切相关的IR聚集在一起，则将其排除，从而产生一个包含96个大IR的集合。其中，24个（25%）发生在X染色体上，尽管它只代表了基因组的5%。在X染色体IR中，83.3%的同源性大于或等于99%，而常染色体IR的同源性为28.8%。来自X染色体的11个IR、来自11染色体的1个IR和已经描述的来自Y染色体的7个IR含有主要在睾丸中表达的基因。对其中8个IR的PCR分析正确扩增了人类基因组中的相应区域，6个IR也被确认为大猩猩或黑猩猩基因组中的疾病。相似性点图显示，22个IR含有进一步的二级同源结构，部分分为三个不同的模式。在X和Y染色体上含有睾丸基因的大的高度同源IR的流行表明在男性生殖系基因表达和/或通过基因转换维持序列完整性中可能起作用。
We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length LIP to 100 kb. This analysis required 6 h oil a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were ill unfinished/unassembled regions of the genome, or Clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred oil the X-chromosome, although it represents only similar to5% of the genome. Of the X-chromosome IRs, 83.3% were greater than or equal to99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed ill gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes oil the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.