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在人类端粒对端粒参考基因组中,对线粒体伪基因 (NUMT) 的全面识别

Yichen Tao¹, Chengpeng He², Deng Lin¹

¹MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.

|November 25, 2023

概括

研究人员在人类完整基因组参考T2T-CHR13中发现的核线粒体DNA段 (NUMT) 比以前所知的更多. 这提高了对线粒体DNA变异的理解,并有助于准确的遗传分析.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

核线粒体DNA细分 (NUMT) 通过模仿真实的线粒体DNA突变来复杂化线粒体研究.
以前的人类参考基因组,如hg38,有不完整的NUMT编译,阻碍了准确的分析.

研究的目的:

在完整的人类参考基因组 (T2T-CHR13) 中全面识别所有固定NUMT.
建立一个真实的线粒体DNA (mtDNA) 突变频谱,以准确识别NUMT.
评估NUMT对像ATAC-seq.q.这样的基因组分析的影响.

主要方法:

利用GeneBank中的人类泛线基因组 (HPMT) 进行NUMT识别.
在多个人类参考基因组中应用更严格的NUMT识别门.
对核基因组进行mtDNA的20-mer对齐.
在具有和没有mtDNA的细胞系上进行了ATAC-seq实验.

主要成果:

在使用HPMT和更严格的门的情况下,在三个人类参考基因组中确定了大约10%的NUMT.
与hg38相比,在T2T-CHR13中观察到NUMT的6%增加,包括染色体臂上的新型NUMT.
在核基因组中检测到许多短的mtDNA类段.
结论NUMT对大量ATAC-seq数据的影响最小,尽管mtDNA衍生读数显著.

结论:

完整的人类参考基因组T2T-CHR13包含的NUMT数量明显高于以前记录的数量.
使用真实的mtDNA光谱准确识别NUMT对于区分真实突变和伪基因至关重要.
对NUMT和mtDNA类段的认识对于优化短安普利康和无细胞mtDNA检测试验至关重要.
在大量的ATAC-seq分析中,NUMT不会显著干扰.

关键词:

ATAC-seqq 的使用情况.这些数字是NUMTS.人类基因组是人类参考基因组.线粒体DNA是线粒体DNA的组成部分.

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