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221 results
2022
Shue Chen, Leah Rosin, Gianluca Pegoraro, Nellie Moshkovich, Patrick Murphy, Guoyun Yu, and Elissa Lei. 2022. “NURF301 Contributes to Gypsy Chromatin Insulator-Mediated Nuclear Organization”. Nucleic Acids Res, 50, 14, Pp. 7906-24. doi:10.1093/nar/gkac600
Shue Chen, Leah Rosin, Gianluca Pegoraro, Nellie Moshkovich, Patrick Murphy, Guoyun Yu, and Elissa Lei. 2022. “NURF301 Contributes to Gypsy Chromatin Insulator-Mediated Nuclear Organization”. Nucleic Acids Res, 50, 14, Pp. 7906-24. doi:10.1093/nar/gkac600
Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three...
Jonathan Zirin, Justin Bosch, Raghuvir Viswanatha, Stephanie Mohr, and Norbert Perrimon. 2022. “State-of-the-Art CRISPR for in Vivo and Cell-Based Studies in Drosophila”. Trends Genet, 38, 5, Pp. 437-53. doi:10.1016/j.tig.2021.11.006
Jonathan Zirin, Justin Bosch, Raghuvir Viswanatha, Stephanie Mohr, and Norbert Perrimon. 2022. “State-of-the-Art CRISPR for in Vivo and Cell-Based Studies in Drosophila”. Trends Genet, 38, 5, Pp. 437-53. doi:10.1016/j.tig.2021.11.006
For more than 100 years, the fruit fly, Drosophila melanogaster, has served as a powerful model organism for biological and biomedical research due to its many genetic and physiological similarities to humans and the availability of sophisticated...
Yifang Liu, Joshua Shing Shun Li, Jonathan Rodiger, Aram Comjean, Helen Attrill, Giulia Antonazzo, Nicholas Brown, Yanhui Hu, and Norbert Perrimon. 2022. “FlyPhoneDB: An Integrated Web-Based Resource for Cell-Cell Communication Prediction in Drosophila”. Genetics, 220, 3. doi:10.1093/genetics/iyab235
Yifang Liu, Joshua Shing Shun Li, Jonathan Rodiger, Aram Comjean, Helen Attrill, Giulia Antonazzo, Nicholas Brown, Yanhui Hu, and Norbert Perrimon. 2022. “FlyPhoneDB: An Integrated Web-Based Resource for Cell-Cell Communication Prediction in Drosophila”. Genetics, 220, 3. doi:10.1093/genetics/iyab235
Multicellular organisms rely on cell-cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell-cell communication pathways can be inferred from transcriptomic datasets based on ligand-receptor...
Jun Xu, Ah-Ram Kim, Ross Cheloha, Fabian Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2022. “Protein Visualization and Manipulation in through the Use of Epitope Tags Recognized by Nanobodies”. Elife, 11. doi:10.7554/eLife.74326
Jun Xu, Ah-Ram Kim, Ross Cheloha, Fabian Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2022. “Protein Visualization and Manipulation in through the Use of Epitope Tags Recognized by Nanobodies”. Elife, 11. doi:10.7554/eLife.74326
Expansion of the available repertoire of reagents for visualization and manipulation of proteins will help understand their function. Short epitope tags linked to proteins of interest and recognized by existing binders such as nanobodies facilitate...
Rohit Singh, Joshua Shing Shun Li, Sudhir Gopal Tattikota, Yifang Liu, Jun Xu, Yanhui Hu, Norbert Perrimon, and Bonnie Berger. 2022. “Optimal Transport Analysis of Single-Cell Transcriptomics Directs Hypotheses Prioritization and Validation”. BioRxiv, Pp. 2022.06.27.497786
Rohit Singh, Joshua Shing Shun Li, Sudhir Gopal Tattikota, Yifang Liu, Jun Xu, Yanhui Hu, Norbert Perrimon, and Bonnie Berger. 2022. “Optimal Transport Analysis of Single-Cell Transcriptomics Directs Hypotheses Prioritization and Validation”. BioRxiv, Pp. 2022.06.27.497786
The explosive growth of regulatory hypotheses from single-cell datasets demands accurate prioritization of hypotheses for in vivo validation, but current computational methods fail to shortlist a high-confidence subset that can be feasibly tested. We...
Justin A. Bosch, Norbert Perrimon, and Christian Dahmann. 2022. “Prime Editing for Precise Genome Engineering in Drosophila”. In Drosophila: Methods and Protocols, Pp. 113-34. New York, NY: Springer US
Justin A. Bosch, Norbert Perrimon, and Christian Dahmann. 2022. “Prime Editing for Precise Genome Engineering in Drosophila”. In Drosophila: Methods and Protocols, Pp. 113-34. New York, NY: Springer US
Editing the Drosophila genome is incredibly useful for gene functional analysis. However, compared to gene knockouts, precise gene editing is difficult to achieve. Prime editing, a recently described CRISPR/Cas9-based technique, has the potential to make...
Jiunn Song, Arda Mizrak, Chia-Wei Lee, Marcelo Cicconet, Zon Weng Lai, Wei-Chun Tang, Chieh-Han Lu, Stephanie E. Mohr, Robert V. Farese, and Tobias C. Walther. 2022. “Identification of Two Pathways Mediating Protein Targeting from ER to Lipid Droplets”. Nature Cell Biol
Jiunn Song, Arda Mizrak, Chia-Wei Lee, Marcelo Cicconet, Zon Weng Lai, Wei-Chun Tang, Chieh-Han Lu, Stephanie E. Mohr, Robert V. Farese, and Tobias C. Walther. 2022. “Identification of Two Pathways Mediating Protein Targeting from ER to Lipid Droplets”. Nature Cell Biol
Pathways localizing proteins to their sites of action are essential for eukaryotic cell organization and function. Although mechanisms of protein targeting to many organelles have been defined, how proteins, such as metabolic enzymes, target from the...
Ah-Ram Kim, Jun Xu, Ross Cheloha, Stephanie E. Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2022. “NanoTag Nanobody Tools for Drosophila In Vitro and In Vivo Studies”. Current Protocols, 2, Pp. e628. doi:https://doi.org/10.1002/cpz1.628
Ah-Ram Kim, Jun Xu, Ross Cheloha, Stephanie E. Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2022. “NanoTag Nanobody Tools for Drosophila In Vitro and In Vivo Studies”. Current Protocols, 2, Pp. e628. doi:https://doi.org/10.1002/cpz1.628
Abstract Nanobodies have emerged as powerful protein-binding tools to uncover protein functions. Using functionalized protein binders, proteins of interest can be visualized, degraded, delocalized, or post-translationally modified in vivo. We recently...
2021
Raghuvir Viswanatha, Enzo Mameli, Jonathan Rodiger, Pierre Merckaert, Fabiana Feitosa-Suntheimer, Tonya Colpitts, Stephanie Mohr, Yanhui Hu, and Norbert Perrimon. 2021. “Bioinformatic and Cell-Based Tools for Pooled CRISPR Knockout Screening in Mosquitos”. Nat Commun, 12, 1, Pp. 6825. doi:10.1038/s41467-021-27129-3
Raghuvir Viswanatha, Enzo Mameli, Jonathan Rodiger, Pierre Merckaert, Fabiana Feitosa-Suntheimer, Tonya Colpitts, Stephanie Mohr, Yanhui Hu, and Norbert Perrimon. 2021. “Bioinformatic and Cell-Based Tools for Pooled CRISPR Knockout Screening in Mosquitos”. Nat Commun, 12, 1, Pp. 6825. doi:10.1038/s41467-021-27129-3
Mosquito-borne diseases present a worldwide public health burden. Current efforts to understand and counteract them have been aided by the use of cultured mosquito cells. Moreover, application in mammalian cells of forward genetic approaches such as...
Thomas Ravenscroft, Jennifer Phillips, Elizabeth Fieg, Sameer Bajikar, Judy Peirce, Jeremy Wegner, Alia Luna, Eric Fox, Yi-Lin Yan, Jill Rosenfeld, Jonathan Zirin, Oguz Kanca, Undiagnosed Diseases Network, Paul Benke, Eric Cameron, Vincent Strehlow, Konrad Platzer, Rami Abou Jamra, Chiara Klöckner, Matthew Osmond, Thomas Licata, Samantha Rojas, David Dyment, Josephine Chong, Sharyn Lincoln, Joan Stoler, John Postlethwait, Michael Wangler, Shinya Yamamoto, Joel Krier, Monte Westerfield, and Hugo Bellen. 2021. “Heterozygous Loss-of-Function Variants Significantly Expand the Phenotypes Associated With Loss of GDF11”. Genet Med, 23, 10, Pp. 1889-1900. doi:10.1038/s41436-021-01216-8
Thomas Ravenscroft, Jennifer Phillips, Elizabeth Fieg, Sameer Bajikar, Judy Peirce, Jeremy Wegner, Alia Luna, Eric Fox, Yi-Lin Yan, Jill Rosenfeld, Jonathan Zirin, Oguz Kanca, Undiagnosed Diseases Network, Paul Benke, Eric Cameron, Vincent Strehlow, Konrad Platzer, Rami Abou Jamra, Chiara Klöckner, Matthew Osmond, Thomas Licata, Samantha Rojas, David Dyment, Josephine Chong, Sharyn Lincoln, Joan Stoler, John Postlethwait, Michael Wangler, Shinya Yamamoto, Joel Krier, Monte Westerfield, and Hugo Bellen. 2021. “Heterozygous Loss-of-Function Variants Significantly Expand the Phenotypes Associated With Loss of GDF11”. Genet Med, 23, 10, Pp. 1889-1900. doi:10.1038/s41436-021-01216-8
PURPOSE: Growth differentiation factor 11 (GDF11) is a key signaling protein required for proper development of many organ systems. Only one prior study has associated an inherited GDF11 variant with a dominant human disease in a family with variable...
Xiangzhao Yue, Yongkang Liang, Zhishuang Wei, Jun Lv, Yongjin Cai, Xiaobin Fan, Wenqing Zhang, and Jie Chen. 2021. “Genome-Wide in Vitro and in Vivo RNAi Screens Reveal Fer3 to Be an Important Regulator of Kkv Transcription in Drosophila”. Insect Sci. doi:10.1111/1744-7917.12954
Xiangzhao Yue, Yongkang Liang, Zhishuang Wei, Jun Lv, Yongjin Cai, Xiaobin Fan, Wenqing Zhang, and Jie Chen. 2021. “Genome-Wide in Vitro and in Vivo RNAi Screens Reveal Fer3 to Be an Important Regulator of Kkv Transcription in Drosophila”. Insect Sci. doi:10.1111/1744-7917.12954
Krotzkopf verkehrt (kkv) is a key enzyme that catalyzes the synthesis of chitin, an important component of the Drosophila epidermis, trachea, and other tissues. Here, we report the use of comprehensive RNA interference (RNAi) analyses to search for kkv...
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, and Erica Larschan. 2021. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data”. Nucleic Acids Res, 49, W1, Pp. W641-W653. doi:10.1093/nar/gkab384
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, and Erica Larschan. 2021. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data”. Nucleic Acids Res, 49, W1, Pp. W641-W653. doi:10.1093/nar/gkab384
Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene...