Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions). Clear transitions were observed in DNA‐methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA‐methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng. 2016;113: 2241–2253. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

• Publication year

  2016

• Venue

  Biotechnology and Bioengineering

• Publication date

  2016-04-29

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1002/bit.25990PMID 27072894PMCID 5006888
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

  2015influential reference
• Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems

  2015cited by this paper
• The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing.

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• RNA-mediated epigenetic regulation of gene expression

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• Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

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• Impact of sequencing depth in ChIP-seq experiments

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• R: A language and environment for statistical computing.

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• Understanding the relationship between DNA methylation and histone lysine methylation

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• Role of epigenetics in expression of recombinant proteins from mammalian cells

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• Quality control Genome maintenance in pluripotent stem cells

  2014influential reference
• Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

  2014cited by this paper
• Digital mRNA profiling of N-glycosylation gene expression in recombinant Chinese hamster ovary cells treated with sodium butyrate.

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• Biopharmaceutical benchmarks 2014

  2014cited by this paper
• Dynamic gene expression for metabolic engineering of mammalian cells in culture.

  2013influential reference
• Chinese hamster genome sequenced from sorted chromosomes

  2013influential reference
• Software for Computing and Annotating Genomic Ranges

  2013influential reference
• Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells

  2013cited by this paper
• The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology.

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

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• Fast gapped-read alignment with Bowtie 2

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• DELLY: structural variant discovery by integrated paired-end and split-read analysis

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• Cellular epigenetic stability and cancer.

  2012cited by this paper
• methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

  2012influential reference
• Chinese hamster genome database: an online resource for the CHO community at www.CHOgenome.org.

  2012cited by this paper
• Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

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• CooVar: Co-occurring variant analyzer

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• ChromHMM: automating chromatin-state discovery and characterization

  2012influential reference
• Qualimap: evaluating next-generation sequencing alignment data

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• Promoter methylation and transgene copy numbers predict unstable protein production in recombinant chinese hamster ovary cell lines

  2011cited by this paper
• SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

  2011influential reference
• Selection of CHO host cell subclones with increased specific antibody production rates by repeated cycles of transient transfection and cell sorting

  2011influential reference
• A mechanistic understanding of production instability in CHO cell lines expressing recombinant monoclonal antibodies

  2011cited by this paper
• Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity.

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• Cutadapt removes adapter sequences from high-throughput sequencing reads

  2011influential reference
• Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

  2011influential reference
• Sequence analysis Advance Access publication June 7, 2011 The variant call format and VCFtools

  2010influential reference
• DNA methylation contributes to loss in productivity of monoclonal antibody-producing CHO cell lines.

  2010cited by this paper
• Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment.

  2010cited by this paper
• CHO‐K1 host cells adapted to growth in glutamine‐free medium by FACS‐assisted evolution

  2010cited by this paper
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009influential reference
• Linking DNA methylation and histone modification: patterns and paradigms

  2009cited by this paper
• Intraclonal Protein Expression Heterogeneity in Recombinant CHO Cells

  2009cited by this paper
• Mining transcriptome data for function–trait relationship of hyper productivity of recombinant antibody

  2009cited by this paper
• Model-based Analysis of ChIP-Seq (MACS)

  2008influential reference
• Transcriptional Profiling of Gene Expression Changes in a PACE-Transfected CHO DUKX Cell Line Secreting High Levels of rhBMP-2

  2008cited by this paper
• Mechanisms of chromosome instability in cancers.

  2006cited by this paper
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• Genetic characterization of CHO production host DG44 and derivative recombinant cell lines.

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  2004cited by this paper
• Stability of protein production from recombinant mammalian cells

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  2001cited by this paper
• Biopharmaceutical benchmarks

  2000cited by this paper
• Bending the rules: Transdifferentiation: Flexibility in Cell Differentiation by T.S. Okada Oxford University Press, 1991. £45.00 (x + 238 pages) ISBN 0 19 854281

  1992cited by this paper
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