The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells

Abstract

Chinese hamster ovary (CHO) cells represent the most commonly used production cell line for therapeutic proteins. By recent genome and transcriptome sequencing a basis was created for future investigations of genotype-phenotype relationships and for improvement of CHO cell productivity and product quality. In this context information is missing about DNA cytosine methylation as a crucial epigenetic modification and an important element in mammalian genome regulation and development. Here, we present the first DNA methylation map of a CHO cell line in single-base resolution that was generated by whole genome bisulfite sequencing combined with gene expression analysis by CHO microarrays. We show CHO DP-12 cells to exhibit global hypomethylation compared to a majority of mammalian methylomes and hypermethylation of CpG-dense regions at gene promoters called CpG islands. We also observed partially methylated domains that cover 62% of the CHO DP-12 cell genome and contain functional clusters of genes. Gene expression analysis showed these clusters to be either highly or weakly expressed with regard to CHO-specific characteristics and hence proves DNA methylation in CHO cells to be an important link between genomics and transcriptomics.

The EF‐1α promoter maintains high‐level transgene expression from episomal vectors in transfected CHO‐K1 cells

“…CMV is prone to transcriptional silencing, which is associated with DNA methylation . Mammalian DNA is predominantly methylated at cytosine bases that are part of CpG dinucleotides . In the CMV promoter, the cytosines at positions 404 and 542 were found to be methylated frequently .…”

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

“…This can be further modified by additional mechanisms, such as the interaction with long non‐coding RNAs or by structural DNA sequences such as matrix associated regions or ubiquitous chromatin opening elements that lead to chromatin remodeling (Brinkman et al, ; Sarkies and Sale, ). So far, these mechanisms were mostly investigated in the context of cancer and developmental biology, so that very little information is currently available on changes in epigenetic regulation in cells maintained in culture (Nestor et al, ; Wippermann et al, ). The concept of changing the epigenome globally, however, has been used to advantage, both for cell line optimisation (Seth et al, ) and for short‐term transcriptome modification to increase recombinant productivity by histone deacetylase inhibitors such as sodium butyrate (Kantardjieff et al, ; Lee et al, ; Liu et al, ).…”

Optimization of Protein Expression in Mammalian Cells

“…For long-term, consistent protein production, it is necessary to stably integrate genes of interest into the genome of the host cell at sites that are transcriptionally active, that do not experience gene silencing, (Wippermann, Rupp, Brinkrolf, Hoffrogge, & Noll, 2015) and are not susceptible to genetic rearrangement (Dorai et al, 2012). Viral vectors target transcriptionally active regions of the genome to integrate their DNA, and they have inbuilt mechanisms to divert the cellular machinery in their favor.…”