Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Università di Bari, Bari 70126, Italy.
BMC Genomics. 2011 Oct 20;12:517. doi: 10.1186/1471-2164-12-517.
Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies.
Here we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications.
We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.
真核核基因组包含称为 NumtS（核线粒体序列）的线粒体 DNA 片段，其插入的方式和时间，以及它们在基因组中的功能/结构作用是有争议的问题。插入位点与染色体断裂匹配，表明非同源末端连接位点通常发生的微缺失在存在 NumtS 时会减少。一些 NumtS 参与导致片段重复的重组事件。此外，NumtS 是多态的，这一特征使它们成为群体标记的候选者。最后，它们是人类 mtDNA 测序过程中污染的原因，导致假异质性的产生。
在这里，我们展示了 RHNumtS.2，这是最详尽的人类 NumtSome 目录，注释了 585 个 NumtS，其中 97%在一个欧洲个体和 HapMap 样本中得到了验证。NumtS 完整数据集和相关特征已在 UCSC 基因组浏览器中提供。生成的序列已提交给 INSDC 数据库。在 UCSC 基因组浏览器中实现 RHNumtS.2 轨道的目的是为了方便浏览 NumtS 轨道，以便在广泛的研究应用中利用它们。
我们旨在为科学界提供最详尽的人类 NumtSome 概述，这是一个资源，旨在支持多种研究应用，例如涉及人类结构变异、多样性和疾病的研究，以及检测假异质性 mtDNA 变体。在实现 NumtS 轨道之后，BLAT 程序在 UCSC 基因组浏览器中的应用现在成为了另一种检查异质性伪影的工具，通过 NumtS 轨道提供的数据支持。
