Population and subspecies diversity at mouse centromere satellites.
Population and subspecies diversity at mouse centromere satellites.
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DOI：
10.1186/s12864-021-07591-5
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发表时间：
2021-04-17
期刊：
影响因子：
4.4
通讯作者：
Dumont BL
中科院分区：
文献类型：
--
作者：
Arora UP;Charlebois C;Lawal RA;Dumont BL
哺乳动物着丝粒是富含卫星的染色质结构域，在动粒组装和染色体分离中起保守作用。着丝粒卫星在物种之间迅速进化，但对这些位点的种群水平多样性知之甚少。我们开发了一种基于k-mer的方法来量化全基因组测序数据中的着丝粒拷贝数和序列变异。我们采用这种方法，不同的近交系和野生家鼠（小家鼠）基因组的轮廓的核心着丝粒（小）卫星和pericentromeric（主要）卫星重复的多样性。我们发现，小卫星拷贝数的变化超过10倍之间的近交系小鼠品系，而主要的卫星拷贝数跨越3倍的范围。与普遍认为的小鼠着丝粒重复序列的同质性的假设相反，我们发现了单个基因组内显著的卫星序列异质性，小卫星的多样性水平超过了大卫星。在野生捕获的小鼠的分析牵连亚种和人口来源的卫星拷贝数和卫星异质性的变化的重要决定因素。有趣的是，我们还发现，野生捕获的小鼠港口显着减少小卫星拷贝数和提高卫星序列的异质性相比，近交系，这表明近亲繁殖可能重塑着丝粒结构在明显的方式。综上所述，我们的研究结果突出了基于k聚体的方法在重复区域探测变异的能力，提供了小家鼠着丝粒变异的初步画像，并为未来对这些基本染色质结构域的自然遗传变异后果的功能研究奠定了基础。在线版本包含补充材料，可通过10.1186/s12864-021-07591-5获得。
Mammalian centromeres are satellite-rich chromatin domains that execute conserved roles in kinetochore assembly and chromosome segregation. Centromere satellites evolve rapidly between species, but little is known about population-level diversity across these loci. We developed a k-mer based method to quantify centromere copy number and sequence variation from whole genome sequencing data. We applied this method to diverse inbred and wild house mouse (Mus musculus) genomes to profile diversity across the core centromere (minor) satellite and the pericentromeric (major) satellite repeat. We show that minor satellite copy number varies more than 10-fold among inbred mouse strains, whereas major satellite copy numbers span a 3-fold range. In contrast to widely held assumptions about the homogeneity of mouse centromere repeats, we uncover marked satellite sequence heterogeneity within single genomes, with diversity levels across the minor satellite exceeding those at the major satellite. Analyses in wild-caught mice implicate subspecies and population origin as significant determinants of variation in satellite copy number and satellite heterogeneity. Intriguingly, we also find that wild-caught mice harbor dramatically reduced minor satellite copy number and elevated satellite sequence heterogeneity compared to inbred strains, suggesting that inbreeding may reshape centromere architecture in pronounced ways. Taken together, our results highlight the power of k-mer based approaches for probing variation across repetitive regions, provide an initial portrait of centromere variation across Mus musculus, and lay the groundwork for future functional studies on the consequences of natural genetic variation at these essential chromatin domains. The online version contains supplementary material available at 10.1186/s12864-021-07591-5.
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影响因子：
21.3
作者：
Bakhoum, Samuel F.;Thompson, Sarah L.;Manning, Amity L.;Compton, Duane A.
通讯作者：
Compton, Duane A.
DOI：
10.1038/nrm2718
发表时间：
2009-07
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
通讯作者：
--
影响因子：
46.9
作者：
Jain M;Olsen HE;Turner DJ;Stoddart D;Bulazel KV;Paten B;Haussler D;Willard HF;Akeson M;Miga KH
通讯作者：
Miga KH
影响因子：
4.4
作者：
Komissarov AS;Gavrilova EV;Demin SJ;Ishov AM;Podgornaya OI
通讯作者：
Podgornaya OI
影响因子：
2.5
作者：
Churchill, Gary A.;Gatti, Daniel M.;Munger, Steven C.;Svenson, Karen L.
通讯作者：
Svenson, Karen L.