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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DOI
Autor*in
Hackl, Matthias; Jakobi, Tobias; Blom, JochenUniBi; Doppmeier, DanielUniBi; Brinkrolf, KarinaUniBi; Szczepanowski, RafaelUniBi; Bernhart, Stephan H; Höner zu Siederdissen, Christian; Bort, Juan A Hernandez; Wieser, Matthias; Kunert, Renate; Jeffs, Simon
Alle
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > AG Genominformatik
Abstract / Bemerkung
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.
Erscheinungsjahr
2011
Zeitschriftentitel
Journal of Biotechnology
Band
153
Ausgabe
1-2
Seite(n)
62-75
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2087955

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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. https://doi.org/10.1016/j.jbiotec.2011.02.011
Hackl, Matthias, Jakobi, Tobias, Blom, Jochen, Doppmeier, Daniel, Brinkrolf, Karina, Szczepanowski, Rafael, Bernhart, Stephan 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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