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Chung, Verena

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Chung, Verena

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Author's Publications: search.filters.isAuthorOfPublication.47dc2654-dceb-47d8-bcc0-b9914daeea79

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    Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data
    (Oxford University Press, 2018) Hu, Yanhui; Vinayagam, Arunachalam; Nand, Ankita; Comjean, Aram; Chung, Verena; Hao, Tong; Mohr, Stephanie; Perrimon, Norbert
    Abstract Model organism and human databases are rich with information about genetic and physical interactions. These data can be used to interpret and guide the analysis of results from new studies and develop new hypotheses. Here, we report the development of the Molecular Interaction Search Tool (MIST; http://fgrtools.hms.harvard.edu/MIST/). The MIST database integrates biological interaction data from yeast, nematode, fly, zebrafish, frog, rat and mouse model systems, as well as human. For individual or short gene lists, the MIST user interface can be used to identify interacting partners based on protein–protein and genetic interaction (GI) data from the species of interest as well as inferred interactions, known as interologs, and to view a corresponding network. The data, interologs and search tools at MIST are also useful for analyzing ‘omics datasets. In addition to describing the integrated database, we also demonstrate how MIST can be used to identify an appropriate cut-off value that balances false positive and negative discovery, and present use-cases for additional types of analysis. Altogether, the MIST database and search tools support visualization and navigation of existing protein and GI data, as well as comparison of new and existing data.
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    A gene-specific T2A-GAL4 library for Drosophila
    (eLife Sciences Publications, Ltd, 2018) Lee, Pei-Tseng; Zirin, Jonathan; Kanca, Oguz; Lin, Wen-Wen; Schulze, Karen L; Li-Kroeger, David; Tao, Rong; Devereaux, Colby; Hu, Yanhui; Chung, Verena; Fang, Ying; He, Yuchun; Pan, Hongling; Ge, Ming; Zuo, Zhongyuan; Housden, Benjamin E; Mohr, Stephanie; Yamamoto, Shinya; Levis, Robert W; Spradling, Allan C; Perrimon, Norbert; Bellen, Hugo J
    We generated a library of ~1000 Drosophila stocks in which we inserted a construct in the intron of genes allowing expression of GAL4 under control of endogenous promoters while arresting transcription with a polyadenylation signal 3’ of the GAL4. This allows numerous applications. First, ~90% of insertions in essential genes cause a severe loss-of-function phenotype, an effective way to mutagenize genes. Interestingly, 12/14 chromosomes engineered through CRISPR do not carry second-site lethal mutations. Second, 26/36 (70%) of lethal insertions tested are rescued with a single UAS-cDNA construct. Third, loss-of-function phenotypes associated with many GAL4 insertions can be reverted by excision with UAS-flippase. Fourth, GAL4 driven UAS-GFP/RFP reports tissue and cell-type specificity of gene expression with high sensitivity. We report the expression of hundreds of genes not previously reported. Finally, inserted cassettes can be replaced with GFP or any DNA. These stocks comprise a powerful resource for assessing gene function.