Copy number variation is associated with gene expression change in archaea.
Copy number variation is associated with gene expression change in archaea.
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DOI：
10.1099/mgen.0.000210
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发表时间：
2018-09
影响因子：
3.9
通讯作者：
Schmid AK
中科院分区：
文献类型：
--
作者：
Dulmage KA;Darnell CL;Vreugdenhil A;Schmid AK
基因组的不稳定性，虽然经常是有害的，也是微生物适应环境变化的一个重要机制。虽然在细菌中进行了广泛的研究，但在古细菌中，基因组不稳定性对生物表型和适应性的影响仍然不清楚。在这里，我们使用DNA分割的方法来检测和量化的基因组范围内的拷贝数变异（CNV）的高通量数据集在一个模型古细菌物种，盐生盐杆菌的大纲要。在整个基因组中鉴定CNV热点。一些热点与基因表达的变化密切相关，表明表型创新的机制。相比之下，其他基因组基因座中的CNV热点保持表达不变，表明某些表型的缓冲。CNVs与基因表达的对应关系通过菌株和条件匹配的转录组学和特定位点的DNA定量实验进行验证。CNV热点位置与已知插入序列（IS）元件位置的显著相关性表明了产生基因组不稳定性的机制。鉴于H. salinarum尽管在单核苷酸水平的稳定性，这些结果表明，基因组可塑性介导的IS元件活动可以提供一个来源的表型创新在极端环境中。
Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
古细胞组蛋白对细胞形态和基因表达的生长期特异性调节。
影响因子：
6.4
作者：
Dulmage KA;Todor H;Schmid AK
通讯作者：
Schmid AK
嗜盐古菌中受调控的多倍体。
影响因子：
3.7
作者：
Breuert S;Allers T;Spohn G;Soppa J
通讯作者：
Soppa J
影响因子：
3.9
作者：
Adams MD;Bishop B;Wright MS
通讯作者：
Wright MS