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Comprehensive Mapping of Functional Enhancers in Chinese Hamster Ovary Cells
María Santos1, Yusuf B Johari2, Laura Biggins3
1Epigenetics Programme, Babraham Institute, Cambridge, UK.
Biotechnology and Bioengineering
|October 3, 2025
Summary
Researchers mapped gene enhancers in Chinese hamster ovary (CHO) cells, identifying thousands of new sequences. This work advances understanding of gene regulation for improved biopharmaceutical production using CHO cell technology.
Area of Science:
- Biotechnology
- Molecular Biology
- Genomics
Background:
- Chinese hamster ovary (CHO) cells are crucial for producing therapeutic proteins.
- Optimizing gene expression in CHO cells is hindered by incomplete knowledge of regulatory mechanisms.
Purpose of the Study:
- To systematically characterize cis-regulatory elements, specifically enhancers, in CHO cells.
- To provide a comprehensive map of functional enhancers for improved biopharmaceutical production.
Main Methods:
- Genome-wide STARR-seq was used to identify active enhancer regions.
- ATAC-seq and histone modification profiles were integrated to analyze chromatin states.
- Deep learning was employed to identify transcription factor binding motifs.
Main Results:
- Thousands of novel enhancer sequences were identified in the CHO cell genome.
- Highly active enhancers matched or exceeded the strength of viral enhancers.
- Accessible and inaccessible enhancers showed distinct genomic locations and gene associations.
- YY1 transcription factor binding motifs were critical for enhancer activity.
Conclusions:
- This study presents the first comprehensive map of validated enhancers in CHO cells.
- Identified enhancers and transcription factor roles offer insights into CHO cell gene regulation.
- Findings provide a foundation for engineering CHO cells to enhance biopharmaceutical production.
