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J Biotechnol. 2014 Nov 20;190:64-75. doi: 10.1016/j.jbiotec.2014.07.437. Epub 2014 Jul 31.

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

Author information

1
Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: tjakobi@cebitec.uni-bielefeld.de.
2
Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: karina.brinkrolf@cebitec.uni-bielefeld.de.
3
Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: tauch@cebitec.uni-bielefeld.de.
4
Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: thomas.noll@uni-bielefeld.de.
5
Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany; Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: jens.stoye@uni-bielefeld.de.
6
Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany. Electronic address: puehler@cebitec.uni-bielefeld.de.
7
Bioinformatik und Systembiologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany. Electronic address: alexander.goesmann@computational.bio.uni-giessen.de.

Abstract

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.

KEYWORDS:

Bioinformatics pipeline; Chinese hamster ovary cells; Promoter analysis; RNA sequencing; Transcription start site identification

PMID:
25086342
DOI:
10.1016/j.jbiotec.2014.07.437
[Indexed for MEDLINE]

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