Morphological complexity. Large-scale fly cell RNAi screen. Breaking report.

Data corresponding to the screen reported in this paper are available at flyrnai.org and through PubChem. The fly cell screen was done in Kc cells. The study includes mammalian cell follow-up.

Yin et al. A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes. Nature Cell Biology (2013) doi:10.1038/ncb2764.

*See also* Olson MF. Finding the shape-shifter genes. Nat Cell Biol. 2013 PMID: 23817235.

GenomeRNAi Update. Breaking Report.

On my desk to read today? This open access update on the DKFZ's GenomeRNAi database of mammalian and Drosophila RNAi screen data.

Schmidt EE, Pelz O, Buhlmann S, Kerr G, Horn T, Boutros M. GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 2012 Nov 27. PubMed PMID: 23193271.

Mammalian RNAi Review

On my desk to ready today? A thought-provoking review on progress made and the future of RNAi as a tool in mammalian cells.

Kaelin WG Jr. Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science. 2012 Jul 27;337(6093):421-2. PubMed PMID: 22837515.

Among the recommendations made for the future of mammalian RNAi is screening of smaller focused gene sets with more unique reagents per gene. The DRSC facilitates a similar approach in Drosophila cell-based RNAi screening via availability of deeper-coverage focused or 'sub' libraries and custom dsRNA synthesis for a set of genes based on our existing collection of templates.

Breaking Report: Review of RNAi screening

Norbert and I have a new review out that discusses cell-based and in vivo RNAi in various species and emphasizes interaction of the RNAi screening field with other fields of study.

Mohr & Perrimon (2011) RNAi screening: new approaches, understandings, and organisms. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna. PubMed ID: 21953743

Breaking Reports: Validation, Screening & in vivo Technologies

On my desk to read today? A couple of new cell-based screen-related papers--one of which systematically tests orthologs of candidate genes culled from fly screens in human cells--and a report on recombinases newly available for use in Drosophila. The report on recombinases is not directly relevant to fly RNAi but I'm including it because what's described should be of general interest to Drosophila researchers--yet another new tool in our ever-growing molecular genetic toolbox.

Bai et al. (2011) Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. BMC Biol. 9(1):54. PMID: 21834987.

Dubrovsky et al. (2011) The Drosophila FTZ-F1 nuclear receptor mediates juvenile hormone activation of E75A gene expression through an intracellular pathway. J Biol Chem. PMID: 21832074.

Nern et al. (2011) Multiple new site-specific recombinases for use in manipulating animal genomes. Proc Natl Acad Sci U S A. PMID: 21831835.

Breaking Report: Review by FAQs--Common Screening Center Questions Clarified

On my desk to read today? A review of common questions posed to screening centers--and answers to the questions--from a center in the UK. Recommended reading for potential screeners and for screening center personnel.

Jiang M et al. (2011) Tales from an academic RNAi screening facility; FAQs. Brief Funct Genomics. 10(4):227-37. PMID: 21527443

The DKFZ's GenomeRNAi turns 5.0

I just learned that the Boutros group at DKFZ has launched a "5.0" version of their GenomeRNAi database. Results from DRSC screens, other fly and mammalian cell-based screens, and fly in vivo screens are searchable at GenomeRNAi. Check it out!

Publications on GenomeRNAi are listed here.

Cross-Species Validation with Live Imaging--Cell Cycle Screen Hits

Also on my desk today? A report from Sironi et al. using living mammalian cell imaging and analysis to follow up on hits from RNAi screens related to the cell cycle performed in other species.

Sironi et al. (2011) Automatic quantification of microtubule dynamics enables RNAi-screening of new mitotic spindle regulators. Cytoskeleton 68:266-278.

Breaking Report: RNAi Pathway & Lysosome-Related Organelles

On my desk to read this morning? A report related to the endogenous biology of the RNAi pathway.

Harris et al. (2011) Cargo sorting to lysosome-related organelles regulates siRNA-mediated gene silencing. J Cell Biol. 194(1):77-87. PMID: 21746852.

Breaking Report: Pathogen Screen

On my desk to read today? A pathogen screen in S2 cells.

Qin et al. (2011) Functional Analysis of Host Factors that Mediate the Intracellular Lifestyle of Cryptococcus neoformans. PLoS Pathog. 7(6):e1002078. PMID: 21698225.

Similar interest in screening a relatively small set of genes? The DRSC will cherry-pick from our collection of high-quality amplicons and make dsRNA for your custom screen.

Breaking Report: RNAi "sensor arrays" and RNAi design

On my desk to read today? A newly reported approach to identification of potent shRNAs.

Fellmann et al. 2011 Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay. Molecular Cell 41:733-746.

Be Ever-Vigilant!

On my desk to read today?

Sigoillot and King (2011) Vigilance and Validation: Keys to Success in RNAi Screening. ACS Chem Biol. 2011 6(1):47-60.

Similar but Different--Comparison of 4 Mammalian RNAi Screens

What's on my desk today? A comparison of the methods used in four mammalian cell RNAi screens investigating HIV-1 host cell factors. Pache et a. (2010) Identifying HIV-1 host cell factors by genome-scale RNAi screening. Methods. doe:10.1016/j.ymeth.2010.07.009.

Breaking Report: Host-Pathogen Interactions

What's on my desk today? A just-published, open access report from Akimana et al. (2010) based on a screen performed at the DRSC.

Akimana et al. (2010) Host Factors Required for Modulation of Phagosome Biogenesis and Proliferation of Francisella tularensis within the Cytosol. PLoS One. 2010 Jun 11;5(6):e11025. PMID: 20552012

Breaking Report: Tiling Arrays to Deconvolve shRNA Pools

What am I reading today? Report of a technical development in the 'mammalian world' of RNAi screening.

Boettcher et al. (2010) Decoding pooled RNAi screens by means of barcode tiling arrays. BMC Genomics. 2010 Jan 5;11(1):7.

Web Wednesday: GenomeRNAi

Todays Web Wednesday featuer: GenomeRNAi, an effort from the Boutros group at DKFZ that reports an update in the most recent database issue of NAR:

Gilsdorf et al. (2009) GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. Nucleic Acids Res. doi: doi:10.1093/nar/gkp1038.

Database issue of NAR 2009 (free online access)

GenomeRNAi

And check out their "List all Screens" for what I assume is a summary of the screens that are searchable in the database. Included among the screens in Drosophila and human cells listed are many published screens based on data obtained at the DRSC. Looks like a good place to go to see what's out there from many groups.

Breaking Report: Metazoan Secretory Pathway

What's on my desk to read today (besides the post-holiday pileup of emails)? A recent report based on a screen performed at the DRSC: Wendler et al. (2009) A genome-wide RNA interference screen identifies two novel components of the metzoan secretory pathway. EMBO Journal. Protocols notes: Luciferase assay readout (stable S2 cell line with the reporter construct), DRSC genome-wide library, follow up in human cells with siRNAs.

Breaking Report: Allele-Specific siRNAs

What's on my desk today? A report with relevance to RNAi reagent design and treatment of genetic diseases: Huang et al. (2009) Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs. NAR. doi:10.1093/nar/gkp835

Breaking Report: RNAi Screen Analysis

Recommended reading:

Birmingham et al. (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009 Aug;6(8):569-75.

PubMed PMID: 19644458.

Grant Opportunity for Mammalian RNAi

Thermo recently announced a grant opportunity for mammalian RNAi screening.