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2. Massively targeted evaluation of therapeutic CRISPR off-targets in cells

Author

Pan, Xiaoguang, Qu, Kunli, Yuan, Hao, Xiang, Xi, Anthon, Christian, Pashkova, Liubov, Liang, Xue, Han, Peng, Corsi, Giulia I., Xu, Fengping, Liu, Ping, Zhong, Jiayan, Zhou, Yan, Ma, Tao, Jiang, Hui, Liu, Junnian, Wang, Jian, Jessen, Niels, Bolund, Lars, Yang, Huanming, Xu, Xun, Church, George M., Gorodkin, Jan, Lin, Lin, and Luo, Yonglun

Published
2022
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5. CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.

Author

Geissler, Adrian Sven, Fehler, Annaleigh Ohrt, Poulsen, Line Dahl, González-Tortuero, Enrique, Kallehauge, Thomas Beuchert, Alkan, Ferhat, Anthon, Christian, Seemann, Stefan Ernst, Rasmussen, Michael Dolberg, Breüner, Anne, Hjort, Carsten, Vinther, Jeppe, and Gorodkin, Jan

Subjects
CRISPRS, BACILLUS subtilis, AMYLASES, GENE expression, CYTOCHROME oxidase, ANTISENSE RNA, OPERONS
Abstract

Yield improvements in cell factories can potentially be obtained by fine-tuning the regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds of putative novel non-coding transcribed regions. Surprisingly, we found among hundreds of non-coding and structured RNA candidates that non-coding genomic regions are proportionally undergoing the highest changes in expression during fermentation. Since these classes of RNA are also understudied, we targeted the corresponding genomic regions with CRIPSRi knockdown to test for any potential impact on the yield. From differentially expression analysis, we selected 53 non-coding candidates. Although CRISPRi knockdowns target both the sense and the antisense strand, the CRISPRi experiment cannot link causes for yield changes to the sense or antisense disruption. Nevertheless, we observed on several instances with strong changes in enzyme yield. The knockdown targeting the genomic region for a putative antisense RNA of the 3′ UTR of the skfA-skfH operon led to a 21% increase in yield. In contrast, the knockdown targeting the genomic regions of putative antisense RNAs of the cytochrome c oxidase subunit 1 (ctaD) , the sigma factor sigH , and the uncharacterized gene yhfT decreased yields by 31 to 43%. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis

Author

Yarani, Reza, primary, Palasca, Oana, additional, Doncheva, Nadezhda T., additional, Anthon, Christian, additional, Pilecki, Bartosz, additional, Svane, Cecilie A. S., additional, Mirza, Aashiq H., additional, Litman, Thomas, additional, Holmskov, Uffe, additional, Bang-Berthelsen, Claus H., additional, Vilien, Mogens, additional, Jensen, Lars J., additional, Gorodkin, Jan, additional, and Pociot, Flemming, additional

Published
2023
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8. CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis

Author

Geissler, Adrian Sven, primary, Fehler, Annaleigh Ohrt, additional, Poulsen, Line Dahl, additional, González-Tortuero, Enrique, additional, Kallehauge, Thomas Beuchert, additional, Alkan, Ferhat, additional, Anthon, Christian, additional, Seemann, Stefan Ernst, additional, Rasmussen, Michael Dolberg, additional, Breüner, Anne, additional, Hjort, Carsten, additional, Vinther, Jeppe, additional, and Gorodkin, Jan, additional

Published
2022
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11. The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

Author

Geissler, Adrian S., primary, Poulsen, Line D., additional, Doncheva, Nadezhda T., additional, Anthon, Christian, additional, Seemann, Stefan E., additional, González-Tortuero, Enrique, additional, Breüner, Anne, additional, Jensen, Lars J., additional, Hjort, Carsten, additional, Vinther, Jeppe, additional, and Gorodkin, Jan, additional

Published
2022
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12. The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

Author

Geissler, Adrian S, primary, Poulsen, Line D, additional, Doncheva, Nadezhda T, additional, Anthon, Christian, additional, Seemann, Stefan E, additional, González-Tortuero, Enrique, additional, Breüner, Anne, additional, Jensen, Lars J, additional, Hjort, Carsten, additional, Vinther, Jeppe, additional, and Gorodkin, Jan, additional

Published
2022
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13. Massively Targeted Evaluation of Therapeutic CRISPR Off-Targets in Cells

Author

Pan, Xiaoguang, primary, Qu, Kunli, additional, Yuan, Hao, additional, Xiang, Xi, additional, Anthon, Christian, additional, Pashkova, Liubov, additional, Liang, Xue, additional, Han, Peng, additional, Corsi, Giulia, additional, Xu, Fengping, additional, Liu, Ping, additional, Zhong, Jiayan, additional, Zhou, Yan, additional, Ma, Tao, additional, Jiang, Hui, additional, Liu, Junnian, additional, Wang, Jian, additional, Jessen, Niels, additional, Bolund, Lars, additional, Yang, Huanming, additional, Xu, Xun, additional, Church, George, additional, Gorodkin, Jan, additional, Lin, Lin, additional, and Luo, Yonglun, additional

Published
2022
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