Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner zu Siederdissen C, Bort JAH, Wieser M, Kunert R, et al. (2011)
Journal of Biotechnology 153(1-2): 62-75.

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Abstract
Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to identify and annotate both conserved and novel CHO miRNAs in the absence of a Chinese hamster genome, we deep-sequenced small RNA fractions of 6 biotechnologically relevant cell lines and mapped the resulting reads to an artificial reference sequence consisting of all known miRNA hairpins. Read alignment patterns and read count ratios of 5' and 3' mature miRNAs were obtained and used for an independent classification into miR/miR* and 5p/3p miRNA pairs and discrimination of miRNAs from other non-coding RNAs, resulting in the annotation of 387 mature CHO miRNAs. The quantitative content of next-generation sequencing data was analyzed and confirmed using qPCR, to find that miRNAs are markers of cell status. Finally, cDNA sequencing of 26 validated targets of miR-17-92 suggests conserved functions for miRNAs in CHO cells, which together with the now publicly available sequence information sets the stage for developing novel RNAi tools for CHO cell engineering.
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Hackl M, Jakobi T, Blom J, et al. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology. 2011;153(1-2):62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S. H., et al. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 153(1-2), 62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S. H., Höner zu Siederdissen, C., Bort, J. A. H., Wieser, M., et al. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology 153, 62-75.
Hackl, M., et al., 2011. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 153(1-2), p 62-75.
M. Hackl, et al., “Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering”, Journal of Biotechnology, vol. 153, 2011, pp. 62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S.H., Höner zu Siederdissen, C., Bort, J.A.H., Wieser, M., Kunert, R., Jeffs, S., Hofacker, I.L., Goesmann, A., Pühler, A., Borth, N., Grillari, J.: Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology. 153, 62-75 (2011).
Hackl, Matthias, Jakobi, Tobias, Blom, Jochen, Doppmeier, Daniel, Brinkrolf, Karina, Szczepanowski, Rafael, Bernhart, Stephan H, Höner zu Siederdissen, Christian, Bort, Juan A Hernandez, Wieser, Matthias, Kunert, Renate, Jeffs, Simon, Hofacker, Ivo L., Goesmann, Alexander, Pühler, Alfred, Borth, Nicole, and Grillari, Johannes. “Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering”. Journal of Biotechnology 153.1-2 (2011): 62-75.
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61 References

Data provided by Europe PubMed Central.

Widespread changes in protein synthesis induced by microRNAs.
Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N., Nature 455(7209), 2008
PMID: 18668040
Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H., Nucleic Acids Res. 38(Database issue), 2010
PMID: 19965774
Genesis: cluster analysis of microarray data.
Sturn A, Quackenbush J, Trajanoski Z., Bioinformatics 18(1), 2002
PMID: 11836235
MicroRNAs as gatekeepers of apoptosis.
Subramanian S, Steer CJ., J. Cell. Physiol. 223(2), 2010
PMID: 20112282
CHO cells adapted to hypothermic growth produce high yields of recombinant beta-interferon.
Sunley K, Tharmalingam T, Butler M., Biotechnol. Prog. 24(4), 2008
PMID: 19194899
Process parameter shifting: Part II. Biphasic cultivation-A tool for enhancing the volumetric productivity of batch processes using Epo-Fc expressing CHO cells.
Trummer E, Fauland K, Seidinger S, Schriebl K, Lattenmayer C, Kunert R, Vorauer-Uhl K, Weik R, Borth N, Katinger H, Muller D., Biotechnol. Bioeng. 94(6), 2006
PMID: 16736532
Isolation of Chinese hamster cell mutants deficient in dihydrofolate reductase activity.
Urlaub G, Chasin LA., Proc. Natl. Acad. Sci. U.S.A. 77(7), 1980
PMID: 6933469
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity.
van der Burgt A, Fiers MW, Nap JP, van Ham RC., BMC Genomics 10(), 2009
PMID: 19405940

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