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

Abstract

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.

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

“…Thus, efforts to define the chromatin states of genes and their regulatory units were error-prone [Feichtinger et al, 2016]. We therefore recalculated the chromatin states for the PICR assembly using the ChiPSeq-derived histone mark reads obtained by Feichtinger et al, (2016).…”

“…We called variants from whole-genome resequencing data for 13 representative resequenced CHO cell lines [Lewis et al, 2013], [Feichtinger et al, 2016] to identify genes that have newly discovered mutations in the RefSeq coding gaps. Each sample has ~300 mutations in coding gaps, 90% of which are SNPs (Supplementary Table S7).…”

“…(a) Chromatin states defined by histone marks: Left: histone marks for CSA assembly [Brinkrolf et al, 2013], [Feichtinger et al, 2016]; center: histone marks for PICR assembly; right: histone marks from the Human Epigenome Project [Kundaje et al, 2015] (b) 1,538 genes associated with mitochondria were blasted from TSS to TES against the CSA and RefSeq assemblies. The number of hits completely found on a single scaffold is displayed for each assembly.…”

“…(d) The 1,011 complete genes found in PICR were extended 5 kb upstream and 1.5 kb downstream to include promoters and other regulatory non-coding regions and blasted against existing assemblies. (e) Chromatin states around three genes as found in the previously published CSA-based chromatin state model [Feichtinger et al, 2016] (top for each gene) and the PICR assembly (bottom for each gene), showing promoter and regulatory elements in addition to active transcription.…”

“…A G->T mutation introduces an early stop codon in exon 1, resulting in a loss in Xylt2 activity. The genotype is shown for a variety of CHO cell lines [Lewis et al, 2013], [Feichtinger et al, 2016], [van Wijk et al, 2017], with only pgsA745 showing the early stop codon.…”