The efforts to obtain genomic resources for the Chinese Hamster in the past decade, from transcriptome and proteome to genome sequencing, have given us a huge trove of data and information for harnessing the potential of CHO cells for biopharmaceuticals production. Recent advances made by the ENCODE project for the human genome have prompted us to explore the transcription regulatory elements outside gene bodies. Using genomic and transcriptomic data from the Chinese Hamster and different CHO cell lines, the CpG-rich regions and conservation of promoter motifs between hamster, mouse and human was examined. We find that many genes with upstream CpG islands show differential expression between producing and non-producing cell lines. The depth of sequencing employed also enabled us to analyze the probability of mutation and other genome variations in cell lines. The availability of such information will open new dimensions for the study and the manipulation of the CHO genome beyond the gene coding sequence.

Beyond the gene body in the Chinese hamster genome

245th National Meeting (2013)

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