Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy.
Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy.
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DOI：
10.1186/s12864-015-1391-x
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发表时间：
2015-03-08
期刊：
影响因子：
4.4
通讯作者：
Andersen MR
中科院分区：
文献类型：
--
作者：
Kaas CS;Kristensen C;Betenbaugh MJ;Andersen MR
DHFR阴性CHO DXB 11细胞系（也称为DUX-B11和DUKX）历史上是第一个用于大规模生产异源蛋白质的CHO细胞系，并且仍然用于生产许多复杂蛋白质。在此，我们提供了CHO DXB 11基因组的基因组序列，测序深度为33 x。总体而言，观察到显著的基因组漂移，有利于GC → AT点突变，与用于生成细胞系的化学诱变策略一致。基因组中每个基因的测序深度在0x、16 x、33 x和49 x覆盖度的测序深度处显示出不同的峰，对应于基因组中0、1、2和3个拷贝的拷贝数。这表明17%的基因是单倍体，揭示了大量的基因可以相对容易地被敲除。此外，在另外8个分析的CHO基因组中（15-20%单倍性），但在中国仓鼠的基因组中不存在这种单倍性趋势。确认CHO DXB 11中dhfr基因为单倍体;具有转录活性，其余等位基因含有G410 C点突变，导致Thr 137 Arg错义突变。我们在CHO DXB 11基因组中发现了约250万个单核苷酸多态性（SNP），44个基因缺失和9357个SNP，这些SNP干扰了3458个基因的编码区。九个CHO基因组的拷贝数变异被映射到中国仓鼠的染色体上，显示每条染色体的独特特征。这些数据表明，与其他染色体相比，染色体1和4在CHO进化过程中似乎更稳定，因此可能为异源基因的敲入提供最有吸引力的着陆平台。我们的研究揭示了CHO DXB 11和CHO细胞中普遍存在的出乎意料的单倍体程度，并强调了迄今为止测序的CHO细胞系中发生的染色体变化。本文的在线版本（doi：10.1186/s12864-015-1391-x）包含补充材料，可供授权用户使用。
The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins. Here we present the genomic sequence of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC → AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing depths of 0x, 16x, 33x and 49x coverage corresponding to a copy number in the genome of 0, 1, 2 and 3 copies. This indicate that 17% of the genes are haploid revealing a large number of genes which can be knocked out with relative ease. This tendency of haploidy was furthermore shown to be present in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find ~2.5 million single nucleotide polymorphisms (SNP’s), 44 gene deletions in the CHO DXB11 genome and 9357 SNP's, which interfere with the coding regions of 3458 genes. Copy number variations for nine CHO genomes were mapped to the chromosomes of the Chinese hamster showing unique signatures for each chromosome. The data indicate that chromosome one and four appear to be more stable over the course of the CHO evolution compared to the other chromosomes thus might presenting the most attractive landing platforms for knock-ins of heterologous genes. Our studies reveal an unexpected degree of haploidy in CHO DXB11 and CHO cells in general and highlight the chromosomal changes that have occurred among the CHO cell lines sequenced to date. The online version of this article (doi:10.1186/s12864-015-1391-x) contains supplementary material, which is available to authorized users.
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作者：
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通讯作者：
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影响因子：
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作者：
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DOI：
10.1107/s0907444908022348
发表时间：
2008-09-01
影响因子：
2.2
作者：
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通讯作者：
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DOI：
10.1073/pnas.79.21.6522
发表时间：
1982-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
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作者：
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通讯作者：
SCHIMKE, RT