TY - JOUR
T1 - Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing
AU - Jakobi, Tobias
AU - Brinkrolf, Karina
AU - Tauch, Andreas
AU - Noll, Thomas
AU - Stoye, Jens
AU - Pühler, Alfred
AU - Goesmann, Alexander
N1 - Publisher Copyright:
© 2014 Elsevier B.V.
PY - 2014/11/1
Y1 - 2014/11/1
N2 - 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.
AB - 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.
KW - Bioinformatics pipeline
KW - Chinese hamster ovary cells
KW - Promoter analysis
KW - RNA sequencing
KW - Transcription start site identification
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U2 - 10.1016/j.jbiotec.2014.07.437
DO - 10.1016/j.jbiotec.2014.07.437
M3 - Article
C2 - 25086342
AN - SCOPUS:84911386294
SN - 0168-1656
VL - 190
SP - 64
EP - 75
JO - Journal of Biotechnology
JF - Journal of Biotechnology
ER -