RNAi screening, double RNAi and multi parametric image assays used to build map of cell cycle regulators

Billmann M, Horn T, Fischer B, Sandmann T, Huber W, Boutros M. A genetic interaction map of cell cycle regulators. Mol Biol Cell. 2016 Feb 24. PMID: 26912791.

From the abstract: "Cell based RNAi is a powerful approach to screen for modulators of many cellular processes. However, resulting candidate gene lists from cell-based assays comprise diverse effectors, both direct and indirect, and further dissecting their functions can be challenging. Here, we screened a genome-wide RNAi library for modulators of mitosis and cytokinesis in Drosophila S2 cells. ... We then characterized ∼300 candidate modifiers further by genetic interaction analysis using double RNAi and a multiparametric, imaging-based assay. ... Our results show that the combination of genome-scale RNAi screening and genetic interaction analysis using process-directed phenotypes provides a powerful two-step approach to assign components to specific pathways and complexes."

RNA pol II Cdk12 identified as an Nrf2 target via RNAi screening in S2 cells

Li X, Chatterjee N, Spirohn K, Boutros M, Bohmann D. Cdk12 Is A Gene-Selective RNA Polymerase II Kinase That Regulates a Subset of the Transcriptome, Including Nrf2 Target Genes. Sci Rep. 2016 Feb 25;6:21455. PMID: 26911346.

From the abstract: "The Nrf2 transcription factor is well conserved throughout metazoan evolution and serves as a central regulator of adaptive cellular responses to oxidative stress. We carried out an RNAi screen in Drosophila S2 cells to better understand the regulatory mechanisms governing Nrf2 target gene expression. This paper describes the identification and characterization of the RNA polymerase II (Pol II) kinase Cdk12 as a factor that is required for Nrf2 target gene expression in cell culture and in vivo. ... We suggest that Cdk12 acts as a gene-selective Pol II kinase that engages a global shift in gene expression to switch cells from a metabolically active state to "stress-defence mode" when challenged by external stress."

Genome-wide cell-based screen related to microtubule bundling and lysosome motility

Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016 Jan 26;14(3):611-20. PMID: 26774481.

Cell-based RNAi screen looks at TGF-beta signaling--methods-focused report

Chen X, Xu L. Genome-Wide RNAi Screening to Dissect the TGF-β Signal Transduction Pathway. Methods Mol Biol. 2016;1344:365-77. PMID: 26520138.

From the abstract: "... Here, we describe a protocol for image-based whole-genome RNAi screening aimed at identifying molecules required for TGF-β signaling into the nucleus. Using this protocol we examined 90% of annotated Drosophila open reading frames (ORF) individually and successfully uncovered several novel factors serving critical roles in the TGF-β pathway. Thus cell-based high-throughput functional genomics can uncover new mechanistic insights on signaling pathways beyond what the classical genetics had revealed."

Cultured Drosophila cells 'humanized' for drug studies--video methods paper

Generating a "Humanized" Drosophila S2 Cell Line Sensitive to Pharmacological Inhibition of Kinesin-5. https://t.co/Cykmii1hlq

— flypapers (@fly_papers) February 11, 2016

Analysis of steroid hormone signaling in 41 Drosophila fly cell lines

Stoiber M, Celniker S, Cherbas L, Brown B, Cherbas P. Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines. G3 (Bethesda). 2016 Jan 15. pii: g3.115.023366. PMID: 26772746.

From the abstract: "Steroid hormones induce cascades of gene activation and repression with transformative effects on cell fate. Steroid transduction plays a major role in the development and physiology of nearly all metazoan species, and in the progression of the most common forms of cancer. Despite the paramount importance of steroids in developmental and translational biology, a complete map of transcriptional response has not been developed for any hormone. In the case of 20-hydroxyecdysone (ecdysone) in Drosophila melanogaster, these trajectories range from apoptosis to immortalization. We mapped the ecdysone transduction network in a cohort of 41 cell lines, the largest such atlas yet assembled. ... This atlas of steroid response reveals organizing principles of gene regulation by a model type II nuclear receptor and lays the foundation for comprehensive and predictive understanding of the ecdysone transduction network in the fruit fly."

in vivo RNAi screen related to chromatin remodeling and assembly factor (CHD1)

Kim S, Bugga L, Hong ES, Zabinsky R, Edwards RG, Deodhar PA, Armstrong JA. An RNAi-Based Candidate Screen for Modifiers of the CHD1 Chromatin Remodeler and Assembly Factor in Drosophila melanogaster. G3 (Bethesda). 2015 Nov 23;6(2):245-54. PMID: 26596648.

From the abstract: "The conserved chromatin remodeling and assembly factor CHD1 (chromodomains, helicase, DNA-binding domain) is present at active genes where it participates in histone turnover and recycling during transcription. In order to gain a more complete understanding of the mechanism of action of CHD1 during development, we created a novel genetic assay in Drosophila melanogaster to evaluate potential functional interactions between CHD1 and other chromatin factors. We found that overexpression of CHD1 results in defects in wing development and utilized this fully penetrant and reliable phenotype to conduct a small-scale RNAi-based candidate screen ..."