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.

Journal Article | Published | English

No fulltext has been uploaded

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. Copyright 2014 Elsevier B.V. All rights reserved.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

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.
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.
This data publication is cited in the following publications:
This publication cites the following data publications:

49 References

Data provided by Europe PubMed Central.

miRBase: annotating high confidence microRNAs using deep sequencing data
Kozomara, Nucleic Acids Res. 42(), 2014
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.
Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO., Nat. Biotechnol. 31(8), 2013
PMID: 23873082
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943
The MTE, a new core promoter element for transcription by RNA polymerase II.
Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT., Genes Dev. 18(13), 2004
PMID: 15231738
Transcriptional regulatory elements in the human genome.
Maston GA, Evans SK, Green MR., Annu Rev Genomics Hum Genet 7(), 2006
PMID: 16719718
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Okazaki, Nature (), 2002
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317
Mammalian RNA polymerase II core promoters: insights from genome-wide studies.
Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA., Nat. Rev. Genet. 8(6), 2007
PMID: 17486122
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters.
Saxonov S, Berg P, Brutlag DL., Proc. Natl. Acad. Sci. U.S.A. 103(5), 2006
PMID: 16432200
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y., Proc. Natl. Acad. Sci. U.S.A. 100(26), 2003
PMID: 14663149
The "initiator" as a transcription control element.
Smale ST, Baltimore D., Cell 57(1), 1989
PMID: 2467742
Identification and characterization of the potential promoter regions of 1031 kinds of human genes.
Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, Suyama A, Sakaki Y, Morishita S, Okubo K, Sugano S., Genome Res. 11(5), 2001
PMID: 11337467
Gnomon – NCBI eukaryotic gene prediction tool
Tatusova, Natl. Cent. Biotechnol. Inform. (), 2010
Massive transcriptional start site analysis of human genes in hypoxia cells.
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, Bentley D, Esumi H, Sugano S., Nucleic Acids Res. 37(7), 2009
PMID: 19237398
EST sequencing for gene discovery in Chinese hamster ovary cells.
Wlaschin KF, Nissom PM, Gatti Mde L, Ong PF, Arleen S, Tan KS, Rink A, Cham B, Wong K, Yap M, Hu WS., Biotechnol. Bioeng. 91(5), 2005
PMID: 16003777
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J., Nat. Biotechnol. 29(8), 2011
PMID: 21804562
A beginner's guide to eukaryotic genome annotation.
Yandell M, Ence D., Nat. Rev. Genet. 13(5), 2012
PMID: 22510764
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells.
Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X., PLoS ONE 9(1), 2014
PMID: 24454679

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 25086342
PubMed | Europe PMC

Search this title in

Google Scholar