Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.
Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.
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DOI：
10.1073/pnas.2102842118
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发表时间：
2021-11-23
影响因子：
11.1
通讯作者：
Tanaka H
中科院分区：
文献类型：
--
作者：
Mouakkad-Montoya L;Murata MM;Sulovari A;Suzuki R;Osia B;Malkova A;Katsumata M;Giuliano AE;Eichler EE;Tanaka H
染色体外环状 DNA (eccDNA) 在癌症等人类疾病中发挥着重要作用，但人们对 eccDNA 对健康人类生物学的影响知之甚少。由于 eccDNA 是核 DNA 的一小部分，因此采用人工扩增来增加 eccDNA 的量，从而导致天然成分的损失。我们开发了一种方法来富集天然状态下的 eccDNA 群体（原始小环状 DNA，nscDNA），并研究了它们在人类基因组中的起源。我们发现，在人类精子中，绝大多数 nscDNA 来自高拷贝基因组区域，包括个体之间变异最大的区域。由于 eccDNA 可以重新整合到染色体中，因此 eccDNA 可能会促进人类遗传变异。染色体外环状DNA（eccDNA）起源于生理和疾病条件下各种人体组织中的线性染色体DNA。 eccDNA 的基因组起源主要是利用体外扩增的 DNA 进行研究的。然而，体外扩增通过扭曲总群体化学计量来掩盖定量信息。此外，分析的重点是来自单拷贝基因组区域的 eccDNA，而来自多拷贝区域的 eccDNA 未被检查。为了解决这些问题，我们在没有体外扩增的情况下分离了 eccDNA（原始小环状 DNA，nscDNA），并通过综合基因组、分子和细胞遗传学方法对群体进行了定量评估。我们的方法成功富集了高达数十千碱基的 nscDNA，并且主要源自多拷贝基因组区域，包括片段重复 (SD)。 SD 占人类基因组的 5%，是拷贝数变异的热点，在精子 nscDNA 中显着过高，源自 SD 的测序读数是整个单拷贝区域的三倍。 SD 在小鼠精子 nscDNA 中的比例也很高，我们估计其占核 DNA 的 0.2%。考虑到 eccDNA 可以整合到染色体中，种系衍生的 nscDNA 可能是基因组多样性的中介。
Extrachromosomal circular DNA (eccDNA) plays a role in human diseases such as cancer, but little is known about the impact of eccDNA in healthy human biology. Since eccDNA is a tiny fraction of nuclear DNA, artificial amplification has been employed to increase eccDNA amounts, resulting in the loss of native compositions. We developed an approach to enrich eccDNA populations at the native state (naïve small circular DNA, nscDNA) and investigated their origins in the human genome. We found that, in human sperm, the vast majority of nscDNA came from high-copy genomic regions, including the most variable regions between individuals. Because eccDNA can be incorporated back into chromosomes, eccDNA may promote human genetic variation. Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA in various human tissues under physiological and disease conditions. The genomic origins of eccDNA have largely been investigated using in vitro–amplified DNA. However, in vitro amplification obscures quantitative information by skewing the total population stoichiometry. In addition, the analyses have focused on eccDNA stemming from single-copy genomic regions, leaving eccDNA from multicopy regions unexamined. To address these issues, we isolated eccDNA without in vitro amplification (naïve small circular DNA, nscDNA) and assessed the populations quantitatively by integrated genomic, molecular, and cytogenetic approaches. nscDNA of up to tens of kilobases were successfully enriched by our approach and were predominantly derived from multicopy genomic regions including segmental duplications (SDs). SDs, which account for 5% of the human genome and are hotspots for copy number variations, were significantly overrepresented in sperm nscDNA, with three times more sequencing reads derived from SDs than from the entire single-copy regions. SDs were also overrepresented in mouse sperm nscDNA, which we estimated to comprise 0.2% of nuclear DNA. Considering that eccDNA can be integrated into chromosomes, germline-derived nscDNA may be a mediator of genome diversity.
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影响因子：
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作者：
Dennis MY;Eichler EE
通讯作者：
Eichler EE
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作者：
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通讯作者：
Salzberg, Steven L.
影响因子：
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作者：
BEVERLEY, SM
通讯作者：
BEVERLEY, SM
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L'Abbate A;Macchia G;D'Addabbo P;Lonoce A;Tolomeo D;Trombetta D;Kok K;Bartenhagen C;Whelan CW;Palumbo O;Severgnini M;Cifola I;Dugas M;Carella M;De Bellis G;Rocchi M;Carbone L;Storlazzi CT
通讯作者：
Storlazzi CT
影响因子：
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作者：
Cohen, S;Yacobi, K;Segal, D
通讯作者：
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