High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome.
High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome.
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DOI：
10.1002/bit.27607
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发表时间：
2021-03
影响因子：
3.8
通讯作者：
O'Callaghan PM
中科院分区：
文献类型：
--
作者：
Bevan S;Schoenfelder S;Young RJ;Zhang L;Andrews S;Fraser P;O'Callaghan PM
中国仓鼠卵巢（CHO）细胞系是生产重组治疗蛋白的数十亿美元生物制药行业的支柱。这些细胞系内的局部染色质组织和表观遗传抑制的作用导致随机整合后不可预测和不稳定的转基因表达。对CHO基因组及其高阶染色质组织的有限知识迄今阻碍了解决这些问题所需的功能基因组学方法。在这里，我们展示了CHOK 1 SV ® 10 E9细胞系内基因组组织的综合三维（3D）图谱，以及改进的、片段较少的CHOK 1 SV 10 E9基因组组装。使用我们的高分辨率染色质构象数据集，我们已经将90%的序列分配给染色体规模的基因组组装。我们的全基因组3D图谱鉴定了更高级的染色质结构，如拓扑相关结构域，结合了我们的染色质可及性数据，以增强活性顺式调控元件的鉴定，并将这些顺式调控元件与3D启动子相互作用组中的靶启动子联系起来。我们通过评估转基因整合位点和两个表型不同的细胞系的3D景观来展示我们改进的功能注释的能力。我们的工作开辟了进一步的新基因组工程目标，有可能为工业生物素生产提供重要的改进，并代表了CHO细胞系开发的重大进展。在这项工作中，Bevan及其同事使用ATAC-Seq，Hi-C和Promoter-Capture Hi-C的组合生成了位点特异性整合（SSI）CHO宿主细胞系的全面3D基因组图谱。这些数据集用于识别更高阶的染色质结构，如拓扑相关结构域（TADs），并将其置于全基因组3D启动子相互作用组的背景下。这些数据集的组合可用于设计细胞工程方法，以改善生物加工环境中的CHO性能。
Chinese hamster ovary (CHO) cell lines are the pillars of a multibillion‐dollar biopharmaceutical industry producing recombinant therapeutic proteins. The effects of local chromatin organization and epigenetic repression within these cell lines result in unpredictable and unstable transgene expression following random integration. Limited knowledge of the CHO genome and its higher order chromatin organization has thus far impeded functional genomics approaches required to tackle these issues. Here, we present an integrative three‐dimensional (3D) map of genome organization within the CHOK1SV® 10E9 cell line in conjunction with an improved, less fragmented CHOK1SV 10E9 genome assembly. Using our high‐resolution chromatin conformation datasets, we have assigned ≈90% of sequence to a chromosome‐scale genome assembly. Our genome‐wide 3D map identifies higher order chromatin structures such as topologically associated domains, incorporates our chromatin accessibility data to enhance the identification of active cis‐regulatory elements, and importantly links these cis‐regulatory elements to target promoters in a 3D promoter interactome. We demonstrate the power of our improved functional annotation by evaluating the 3D landscape of a transgene integration site and two phenotypically different cell lines. Our work opens up further novel genome engineering targets, has the potential to inform vital improvements for industrial biotherapeutic production, and represents a significant advancement for CHO cell line development. In this work Bevan and colleagues generate a comprehensive 3D genome map of a site‐specific integration (SSI) CHO host cell line using a combination of ATAC‐Seq, Hi‐C, and Promoter‐Capture Hi‐C. These datasets are used to identify higher order chromatin structures such as topologically‐associated domains (TADs), and puts them in the context of a genome‐wide 3D promoter interactome. The combination of such datasets may be used to design cell engineering approaches for improving CHO performance in the bioprocessing environment.
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影响因子：
64.8
作者：
Jin, Fulai;Li, Yan;Dixon, Jesse R.;Selvaraj, Siddarth;Ye, Zhen;Lee, Ah Young;Yen, Chia-An;Schmitt, Anthony D.;Espinoza, Celso A.;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
48
作者：
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通讯作者：
Salzberg, Steven L.
影响因子：
3.8
作者：
Feichtinger, Julia;Hernandez, Inmaculada;Fischer, Christoph;Hanscho, Michael;Auer, Norbert;Hackl, Matthias;Jadhav, Vaibhav;Baumann, Martina;Krempl, Peter M.;Schmidl, Christian;Farlik, Matthias;Schuster, Michael;Merkel, Angelika;Sommer, Andreas;Heath, Simon;Rico, Daniel;Bock, Christoph;Thallinger, Gerhard G.;Borth, Nicole
通讯作者：
Borth, Nicole
影响因子：
3.8
作者：
Rupp O;MacDonald ML;Li S;Dhiman H;Polson S;Griep S;Heffner K;Hernandez I;Brinkrolf K;Jadhav V;Samoudi M;Hao H;Kingham B;Goesmann A;Betenbaugh MJ;Lewis NE;Borth N;Lee KH
通讯作者：
Lee KH
影响因子：
64.5
作者：
Dowen JM;Fan ZP;Hnisz D;Ren G;Abraham BJ;Zhang LN;Weintraub AS;Schujiers J;Lee TI;Zhao K;Young RA
通讯作者：
Young RA