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

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Mammalian genomes exhibit regional differences in accessibility to transcriptional machinery.
• The integration site of transgenes significantly impacts their transcriptional activity.
• Super-enhancers are highly accessible genomic regions identified as potent regulatory elements influencing cell identity.

Purpose of the Study:

• To investigate the relationship between genomic accessibility, super-enhancers, and gene expression in Chinese hamster ovary (CHO) cells.
• To evaluate the impact of transgene integration site selection on therapeutic protein production.

Main Methods:

• Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) to identify super-enhancers in CHO cells.
• Analysis of gene expression levels in relation to genomic accessibility.
• Lentiviral reporter integration assays to assess expression based on integration site.
• Targeted integration of an IgG vector into a specific super-enhancer region.

Main Results:

• Genes near super-enhancers showed high transcript levels, enriched for oncogenic signaling and proliferation.
• Genes in inaccessible genomic regions exhibited low transcriptional activity and were enriched for remote tissue functions.
• Integration into super-enhancer regions resulted in higher reporter expression compared to inaccessible regions.
• Targeted integration into the Plec super-enhancer yielded high expression of an immunoglobulin light chain gene.

Conclusions:

• The epigenomic landscape of CHO cells, particularly super-enhancers, can guide the selection of optimal transgene integration sites.
• Strategic integration site selection can enhance the development of cell lines for therapeutic protein production.