Epigenomic features revealed by ATAC‐seq impact transgene expression in CHO cells

Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super‐enhancers have been recently described as strong regulatory elements that shape cell identity. Super‐enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase‐Accessible Chromatin Sequencing (ATAC‐seq). Genes near super‐enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super‐enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super‐enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production. The epigenetic context of the integration site of a transgene affects its transcription level. In this study the authors use ATAC‐seq to identify two features, super‐enhancers and inaccessible regions, which respectively enhance and inhibit transgene expression in CHO cells. CRISPR/Cas9 was used to generate single‐copy IgG‐producing clones near a super‐enhancer to demonstrate the utility of these genomic regions for bioprocess applications.