A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells
Autor: | Gyun Min Lee, Isaac Shamie, Kai Xiong, Sascha H. Duttke, Hooman Hefzi, Claudia Z. Han, Jenhan Tao, Shangzhong Li, Karen Julie la Cour Karottki, Anders Holmgaard Hansen, Christopher Benner, Samuel J. Roth, Helene Faustrup Kildegaard, Christopher K. Glass, Nathan E. Lewis |
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Rok vydání: | 2021 |
Předmět: |
AcademicSubjects/SCI01140
AcademicSubjects/SCI01060 TATA box 1.1 Normal biological development and functioning AcademicSubjects/SCI00030 Hamster Standard Article Computational biology Biology AcademicSubjects/SCI01180 Chinese hamster Genome engineering 03 medical and health sciences 0302 clinical medicine Structural Biology Genetics Enhancer Molecular Biology Gene 030304 developmental biology Regulation of gene expression 0303 health sciences Applied Mathematics Chinese hamster ovary cell Human Genome biology.organism_classification Computer Science Applications AcademicSubjects/SCI00980 Generic health relevance 030217 neurology & neurosurgery Biotechnology |
Zdroj: | NAR genomics and bioinformatics, vol 3, iss 3 Shamie, I, Duttke, S H, Karottki, KJC, Han, C Z, Hansen, AH, Hefzi, H, Xiong, K, Li, S, Roth, SJ, Tao, J, Lee, GM, Glass, CK, Kildegaard, HF, Benner, C & Lewis, NE 2021, ' A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells ', NAR Genomics and Bioinformatics, vol. 3, no. 3 . https://doi.org/10.1093/nargab/lqab061 NAR Genomics and Bioinformatics |
Popis: | Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies. |
Databáze: | OpenAIRE |
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