Primate genome architecture influences structural variation mechanisms and functional consequences
Primate genome architecture influences structural variation mechanisms and functional consequences
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DOI：
10.1073/pnas.1305904110
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发表时间：
2013-09-24
影响因子：
11.1
通讯作者：
Korbel, Jan O.
中科院分区：
文献类型：
--
作者：
Gokcumen, Omer;Tischler, Verena;Korbel, Jan O.
虽然基因组结构变异（SV）的核苷酸解析图提供了对人类表型多样性的起源和影响的见解，但迄今为止还缺乏非人类灵长类动物的可比图谱。使用大规模并行DNA测序，我们构建了五只黑猩猩，五只猩猩和五只恒河猴的精细分辨率基因组结构变异图。SV图谱由数千个缺失、重复和移动的元件插入组成，揭示了与类人猿相比，猕猴的反转录转座活性较高。相比之下，非等位基因同源重组在类人猿中特别活跃，这与类人猿和猕猴基因组之间的结构差异有关。在非人类灵长类动物和人类的转录组分析揭示了物种特异性的全基因复制对基因表达的影响。我们确定了13个基因重复与组织特异性基因表达的物种特异性增益相一致，这与基因重复在促进多样化和获得独特功能中的作用相一致。我们的研究揭示了SV形成机制在当今活动中的差异，这可能有助于巨猿和旧大陆猴谱系的持续多样化和适应。
Although nucleotide resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact of phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing, we constructed fine-resolution genomic structural variation maps in five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, which are comprised of thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques compared with great apes. By comparison, nonallelic homologous recombination is specifically active in the great apes, which is correlated with architectural differences between the genomes of great apes and macaque. Transcriptome analyses across nonhuman primates and humans revealed effects of species-specific whole-gene duplication on gene expression. We identified 13 gene duplications coinciding with the species-specific gain of tissue-specific gene expression in keeping with a role of gene duplication in the promotion of diversification and the acquisition of unique functions. Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages.