The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.
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DOI：
10.1186/1471-2164-9-267
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发表时间：
2008-06-03
期刊：
影响因子：
4.4
通讯作者：
Attimonelli M
中科院分区：
文献类型：
--
作者：
Lascaro D;Castellana S;Gasparre G;Romeo G;Saccone C;Attimonelli M
在或多或少的程度上，真核生物的核基因组含有线粒体基因组对应的片段，这些片段来自于随机插入的受损mtDNA片段。NumtS（核mt序列）在所有物种中并不同样丰富，并且在拷贝数方面是冗余的和多态的。在人口和临床遗传学中，对NumtS的数量和位置有一个完整的概述是很重要的。在PubMed上搜索NumtS或线粒体伪基因会产生数百篇报告通过计算机或湿实验室方法生成的人类NumtS汇编的论文。对已发表的汇编的比较清楚地表明，由于生物信息学方法的不明智应用和尚未正确组装的核基因组，数据之间存在显著差异。为了优化NumtS的定量和定位，我们通过应用各种生物信息学方法制作了人类NumtS的共识汇编。应用数据库相似度搜索方法可以实现numt的定位和量化：我们应用了Blastn、MegaBlast和BLAT等多种方法，同时改变参数和数据库；将结果与已发表的汇编进行比较，进一步分析和检查，从而产生参考人类Numt序列（RHNumtS）汇编。得到的numt总数为190。RHNumtS编译代表了一个高度可靠的参考基础，它允许设计一个实验室协议来测试每个numt的实际存在。本文报道了从评分较低的RHNumtS中选择41个NumtS进行PCR扩增和测序的初步结果。与此同时，我们目前正在设计RHNumtS数据库结构，以便在HmtDB资源中实现。将来，同样的数据库将容纳来自其他生物体的NumtS汇编，但只有当特定生物体的核基因组达到高质量的组装水平时，这些汇编才会产生。
To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences) are not equally abundant in all species, and are redundant and polymorphic in terms of copy number. In population and clinical genetics, it is important to have a complete overview of NumtS quantity and location. Searching PubMed for NumtS or Mitochondrial pseudo-genes yields hundreds of papers reporting Human NumtS compilations produced by in silico or wet-lab approaches. A comparison of published compilations clearly shows significant discrepancies among data, due both to unwise application of Bioinformatics methods and to a not yet correctly assembled nuclear genome. To optimize quantification and location of NumtS, we produced a consensus compilation of Human NumtS by applying various bioinformatics approaches. Location and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published compilations, thus producing the Reference Human Numt Sequences (RHNumtS) compilation. The resulting NumtS total 190. The RHNumtS compilation represents a highly reliable reference basis, which may allow designing a lab protocol to test the actual existence of each NumtS. Here we report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from RHNumtS among those with lower score. In parallel, we are currently designing the RHNumtS database structure for implementation in the HmtDB resource. In the future, the same database will host NumtS compilations from other organisms, but these will be generated only when the nuclear genome of a specific organism has reached a high-quality level of assembly.
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影响因子：
3
作者：
Attimonelli, M;Accetturo, M;Tommaseo-Ponzetta, M
通讯作者：
Tommaseo-Ponzetta, M
影响因子：
7
作者：
Costantini, M;Clay, O;Bernardi, G
通讯作者：
Bernardi, G
影响因子：
5.6
作者：
JACOBS, HT;POSAKONY, JW;DAVIDSON, EH
通讯作者：
DAVIDSON, EH
影响因子：
64.8
作者：
GELLISSEN, G;BRADFIELD, JY;WYATT, GR
通讯作者：
WYATT, GR
影响因子：
10.7
作者：
Behura, Susanta K.
通讯作者：
Behura, Susanta K.