Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements
Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements
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DOI：
10.1101/gr.1929904
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发表时间：
2004-02-01
期刊：
影响因子：
7
通讯作者：
Larionov, V
中科院分区：
文献类型：
--
作者：
Leem, SH;Kouprina, N;Larionov, V
报道的人类基因组序列包括约 400 个未知序列缺口，这些缺口在用于基因组测序的细菌人工染色体 (BAC) 和粘粒文库中未发现。这些缺失的序列相当于人类基因组中 1% 的常染色质区域。间隙填充是一个费力的过程，因为它依赖于对大量基因组 BAC 或粘粒文库的随机克隆的分析。在这项工作中，我们证明通过选择性重组捕获酵母中缺失的染色体片段可以加速缩小差距。这两种方法的使用使我们能够闭合人类 19 号染色体上剩余的四个缺口。对缺口序列的分析表明，它们包含多种异常，可能导致微生物宿主中的序列不稳定，包括大块微卫星和小卫星以及高密度的 Alu 重复序列。对 BAC 和 YAC 形式的间隙区域进行测序，使我们能够生成四个基因的完整序列，包括神经元细胞信号基因 SCK1/SLI。SCK1/SLI 基因包含创纪录数量的小卫星，其中大多数是多态性的，并通过孟德尔遗传的减数分裂传递。总之，在酵母中使用替代重组克隆系统可能会大大加速缩小人类基因组（以及其他复杂基因组）中剩余空白的工作，以实现注释所有人类基因的目标。
The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to similar to1% of euchromatic regions of the human genome. Gap filling is a laborious process because it relies on analysis of random clones of numerous genomic BAC or cosmid libraries. In this work we demonstrate that closing the gaps can be accelerated by a selective recombinational capture of missing chromosomal segments in yeast. The use of both methodologies allowed us to close the four remaining gaps on the human chromosome 19. Analysis of the gap sequences revealed that they contain several abnormalities that could result in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of Alu repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI The SCK1/SLI gene contains a record number of minisatellites, most of which are polymorphic and transmitted through meiosis following a Mendelian inheritance. In conclusion, the use of the alternative recombinational cloning system in yeast may greatly accelerate work on closing the remaining gaps in the human genome (as well as in other complex genomes) to achieve the goal of annotation of all human genes.