Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing

Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014)
Journal of Biotechnology 190: 64-75.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Chinese hamster ovary (CHO) cell lines are one of the major production tools for monoclonal antibodies, recombinant proteins, and therapeutics. Although many efforts have significantly improved the availability of sequence information for CHO cells in the last years, forthcoming draft genomes still lack the information depth known from the mouse or human genomes. Many genes annotated for CHO cells and the Chinese hamster reference genome still are in silico predictions, only insufficiently verified by biological experiments. The correct annotation of transcription start sites (TSSs) is of special interest for CHO cells, as these directly define the location of the eukaryotic core promoter. Our study aims to elucidate these largely unexplored regions, trying to shed light on promoter landscapes in the Chinese hamster genome. Based on a 5' enriched dual library RNA sequencing approach 6547 TSSs were identified, of which over 90% were assigned to known genes. These TSSs were used to perform extensive promoter studies using a novel, modular bioinformatics pipeline, incorporating analyses of important regulatory elements of the eukaryotic core promoter on per-gene level and on genomic scale. Copyright 2014 Elsevier B.V. All rights reserved.
Stichworte
Transcription start site identification; Chinese hamster ovary cells; Bioinformatics pipeline; RNA sequencing; Promoter analysis
Erscheinungsjahr
2014
Zeitschriftentitel
Journal of Biotechnology
Band
190
Seite(n)
64-75
ISSN
0168-1656
eISSN
1873-4863
Page URI
https://pub.uni-bielefeld.de/record/2685988

Zitieren

Jakobi T, Brinkrolf K, Tauch A, et al. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology. 2014;190:64-75.
Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A., & Goesmann, A. (2014). Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology, 190, 64-75. doi:10.1016/j.jbiotec.2014.07.437
Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A., and Goesmann, A. (2014). Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology 190, 64-75.
Jakobi, T., et al., 2014. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology, 190, p 64-75.
T. Jakobi, et al., “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”, Journal of Biotechnology, vol. 190, 2014, pp. 64-75.
Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A., Goesmann, A.: Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology. 190, 64-75 (2014).
Jakobi, Tobias, Brinkrolf, Karina, Tauch, Andreas, Noll, Thomas, Stoye, Jens, Pühler, Alfred, and Goesmann, Alexander. “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”. Journal of Biotechnology 190 (2014): 64-75.

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