Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Lewis, Nathan E.; Liu, Xin; Li, Yuxiang; Nagarajan, Harish; Yerganian, George; O’Brien, Edward J.; Bordbar, Aarash; Roth, Anne M; Rosenbloom, Jeffrey; Bian, Chao; Xie, Min; Chen, Wenbin; Li, Ning; Baycin-Hizal, Deniz; Latif, Haythem; Förster, Jochen; Betenbaugh, Michael J; Famili, Iman; Xu, Xun; Wang, Jun; Palsson, Bernhard Ø.

doi:10.1038/nbt.2624

Cited by 343 publications

(331 citation statements)

References 67 publications

(77 reference statements)

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“…In two independent previous attempts, the Chinese hamster genome was generated using Illumina sequencing from DNA isolated from liver tissue acquired from the same hamster colony as used for deriving CHO cells in 1957 [Brinkrolf et al, 2013], [Lewis et al, 2013]. The current RefSeq assembly originated from whole-genome libraries with varying insert sizes [Lewis et al, 2013].…”

Section: Resultsmentioning

confidence: 99%

“…The current RefSeq assembly originated from whole-genome libraries with varying insert sizes [Lewis et al, 2013]. A second assembly (CSA) using chromosome sorted sequencing libraries is also publicly available [Brinkrolf et al, 2013].…”

Section: Resultsmentioning

confidence: 99%

“…However, the longer PacBio SMRT reads and the larger Illumina insert libraries should provide unique strengths that could be captured through assembly merging. Therefore, we aligned the scaffolds and contigs from four independent assemblies: the Illumina-based chromosome sorted assembly (CSA) [Brinkrolf et al, 2013], the RefSeq assembly [Lewis et al, 2013], the pooled Illumina assembly developed here, and our de novo uncurated PacBio SMRT assembly. The Metassembler tool [Wences and Schatz, 2015] uses the first assembly provided as the base and subsequently merges additional assemblies.…”

Section: Resultsmentioning

confidence: 99%

“…We mapped the sequences between the mouse transcription start site (TSS) to transcription end site (TES) against the PICR metassembly, the RefSeq assembly, and the CSA [Lewis et al, 2013], [Brinkrolf et al, 2013]. Genes were called present if both the TSS and TES were found on the same scaffold.…”

Section: Resultsmentioning

confidence: 99%

“…The history of CHO cells dates back to the 1950s when ovarian connective tissue was harvested from the Chinese hamster and derivative cells spontaneously became immortal [Tjio and Puck, 1958]. Since then, CHO has diverged into different adherent and suspension cell lines, such as CHO-K1, CHO-S, and CHO DG44 [Lewis et al, 2013]. Their protein production capacity has been greatly enhanced through decades of refinements in bioprocessing strategies, media optimization, and engineering of transgenes and expression vectors.…”

Section: Introductionmentioning

confidence: 99%

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A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

117

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

117

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Rapid Assays for Lectin Toxicity and Binding Changes that Reflect Altered Glycosylation in Mammalian Cells

Stanley

Sundaram

2014

CP Chemical Biology

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Glycosylation engineering is used to generate glycoproteins, glycolipids, or proteoglycans with a more defined complement of glycans on their glycoconjugates. For example, a mammalian cell glycosylation mutant lacking a specific glycosyltransferase generates glycoproteins, and/or glycolipids, and/or proteoglycans with truncated glycans missing the sugar transferred by that glycosyltransferase, as well as those sugars that would be added subsequently. In some cases, an alternative glycosyltransferase may then use the truncated glycans as acceptors, thereby generating a new or different glycan subset in the mutant cell. Another type of glycosylation mutant arises from gain‐of‐function mutations that, for example, activate a silent glycosyltransferase gene. In this case, glycoconjugates will have glycans with additional sugar(s) that are more elaborate than the glycans of wild type cells. Mutations in other genes that affect glycosylation, such as nucleotide sugar synthases or transporters, will alter the glycan complement in more general ways that usually affect several types of glycoconjugates. There are now many strategies for generating a precise mutation in a glycosylation gene in a mammalian cell. Large‐volume cultures of mammalian cells may also generate spontaneous mutants in glycosylation pathways. This article will focus on how to rapidly characterize mammalian cells with an altered glycosylation activity. The key reagents for the protocols described are plant lectins that bind mammalian glycans with varying avidities, depending on the specific structure of those glycans. Cells with altered glycosylation generally become resistant or hypersensitive to lectin toxicity, and have reduced or increased lectin or antibody binding. Here we describe rapid assays to compare the cytotoxicity of lectins in a lectin resistance test, and the binding of lectins or antibodies by flow cytometry in a glycan‐binding assay. Based on these tests, glycosylation changes expressed by a cell can be revealed, and glycosylation mutants classified into phenotypic groups that may reflect a loss‐of‐function or gain‐of‐function mutation in a specific gene involved in glycan synthesis. Curr. Protoc. Chem. Biol. 6:117‐133 © 2014 by John Wiley & Sons, Inc.

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Emerging Alternative Production Systems

Jostock¹

2007

Handbook of Therapeutic Antibodies

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Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Cited by 343 publications

References 67 publications

A reference genome of the Chinese hamster based on a hybrid assembly strategy

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rapid Assays for Lectin Toxicity and Binding Changes that Reflect Altered Glycosylation in Mammalian Cells

Emerging Alternative Production Systems

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