FlyBook review on RNAi screening in Drosophila cells and in vivo

Heigwer F, Port F, Boutros M. RNA Interference (RNAi) Screening in Drosophila. Genetics. 2018 Mar;208(3):853-874. PMID: 29487145.

From the abstract: "... RNA interference (RNAi) ... has had an important impact on identifying and characterizing gene function. First discovered in Caenorhabditis elegans, RNAi can be used to silence the expression of genes through introduction of exogenous double-stranded RNA into cells. In Drosophila, RNAi has been applied in cultured cells or in vivo to perturb the function of single genes or to systematically probe gene function on a genome-wide scale. In this review, we will describe the use of RNAi to study gene function in Drosophila with a particular focus on high-throughput screening methods applied in cultured cells. ..."

Methods reviews for in vivo RNAi screening in Drosophila

Four! RNAi-relevant methods papers in the recent Drosophila-focused issue of Methods in Molecular Biology:

Billmann M, Boutros M. Methods for High-Throughput RNAi Screening in Drosophila Cells. Methods Mol Biol. 2016;1478:95-116. PMID: 27730577.

Kaya-Çopur A, Schnorrer F. A Guide to Genome-Wide In Vivo RNAi Applications in Drosophila. Methods Mol Biol. 2016;1478:117-143. PMID: 27730578.

Zhou J, Tong C. Design and Methods of Large-Scale RNA Interference Screens in Drosophila. Methods Mol Biol. 2016;1470:163-9. PMID: 27581292. 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.

IMP integrative tool for functional genomics updated to 2.0 version

Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 2015 May 12. PMID: 25969450.

From the abstract: "... IMP 2.0 integrates updated prior knowledge and data collections from the last three years in the seven supported organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Caenorhabditis elegans, and Saccharomyces cerevisiae) and extends function prediction coverage to include human disease. ... Additionally, IMP 2.0 implements a new flexible platform for experts to generate custom hypotheses about biological processes or diseases, making sophisticated data-driven methods easily accessible to researchers. IMP does not require any registration or installation and is freely available for use at http://imp.princeton.edu."

Using phylogenetic relationships to predict protein functions--Sadreyev et al. release PhyloGene

In the 'not RNAi (or CRISPR) but might be of interest to blog readers anyway' department:

Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y. PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. Nucleic Acids Res. 2015 May 9. pii: gkv452. PMID: 25958392.

From the abstract: "... Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. ..."

Genome-wide in vivo RNAi and data integration featured in study on intestinal stem cell regulation

Zeng X, Han L, Singh SR, Liu H, Neumüller RA, Yan D, Hu Y, Liu Y, Liu W, Lin X, Hou SX. Genome-wide RNAi Screen Identifies Networks Involved in Intestinal Stem Cell Regulation in Drosophila. Cell Rep. 2015 Feb 17. pii: S2211-1247(15)00076-5. PMID: 25704823.

From the abstract: "... To comprehensively identify genes and pathways that regulate ISC fates, we performed a genome-wide transgenic RNAi screen in adult Drosophila intestine and identified 405 genes that regulate ISC maintenance and lineage-specific differentiation. By integrating these genes into publicly available interaction databases, we further developed functional networks that regulate ..."

Full-genome screen related to functional insulators

Another full-genome DRSC screen published--congrats!

Fig. 1 from the Bohla et al. paper.

Bohla D, Herold M, Panzer I, Buxa MK, Ali T, Demmers J, Krüger M, Scharfe M, Jarek M, Bartkuhn M, Renkawitz R. A Functional Insulator Screen Identifies NURF and dREAM Components to Be Required for Enhancer-Blocking. PLoS One. 2014 Sep 23;9(9):e107765. PubMed PMID: 25247414; PubMed Central PMCID: PMC4172637.

From the abstract: "... Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. ..."

Integer linear optimization approach to signaling network construction based on protein-protein interaction and RNAi data sets

Ozsoy OE, Can T. A divide and conquer approach for construction of large-scale signaling networks from PPI and RNAi data using linear programming. IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):869-83. PMID: 24334382.

From the abstract: "... In this paper, we propose an integer linear optimization (ILP) model for reconstruction of signaling networks from RNAi data and a reference network. ..."

Related approaches available as online tools at the DRSC include COMPLEAT and SignedPPI

Genome-wide RNAi screen in fly and mammalian systems related to Parkinson's disease

Ivatt RM, Whitworth AJ. SREBF1 links lipogenesis to mitophagy and sporadic Parkinson disease. Autophagy. 2014 Jun 27;10(8). Review. PubMed PMID: 24991824.

From the abstract: "Mitochondrial quality control has an impact on many diseases, but intense research has focused on the action of 2 genes linked to heritable forms of Parkinson disease (PD), PINK1 and PARK2/parkin, which act in a common pathway to promote mitophagy. However, criticism has been raised that little evidence links this mechanism to sporadic PD. To gain a greater insight into the mechanisms of PINK1-PARK2 mediated mitophagy, we undertook a genome-wide RNAi screen in Drosophila and human cell models. ... Our findings suggest a role for lipid synthesis in PINK1-PARK2 mediated mitophagy, and propose a mechanistic link between familial and sporadic PD, supporting a common etiology."

DRSC and collaborators present Online GESS

Yilmazel B, Hu Y, Sigoillot F, Smith JA, Shamu CE, Perrimon N, Mohr SE. Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. BMC Bioinformatics. 2014 Jun 17;15:192. PMID: 24934636; PMCID: PMC4073188.

From the abstract: "... Online GESS provides a straightforward user interface for genome-wide seed region analysis for human, mouse and Drosophila RNAi screen data. With the tool, users can either use a built-in database or provide a database of transcripts for analysis. This makes it possible to analyze RNAi data from any organism for which the user can provide transcript sequences."

Review--Functional Genomics Resources

My co-authors and I are pleased to present this Genetics journal "toolbox" series review article.

Mohr SE, Hu Y, Kim K, Housden BE, Perrimon N. Resources for Functional Genomics Studies in Drosophila melanogaster. Genetics. PubMed PMID: 24653003.

Please note that the final published version is now available--complete with live links to the many websites and online software tools we refer to.

Review--RNAi screening and signaling networks

Evans L, Sailem H, Vargas PP, Bakal C. Inferring signalling networks from images. J Microsc. 2013 Oct;252(1):1-7. PMID: 23841886.

From the abstract:  "This review describes the methodology used to map signalling networks using data generated in the context of RNAi screens."

Luciferase-based assays in cultured cells

Yun C, Dasgupta R. Luciferase reporter assay in Drosophila and Mammalian tissue culture cells. Curr Protoc Chem Biol. 2014 Mar 14;6(1):7-23. PMID: 24652620.

Methods paper on fly RNAi in cells and in vivo

Humbly offered by your blog author ...


Mohr SE. RNAi screening in Drosophila cells and in vivo. Methods. 2014 Feb 24. pii: S1046-2023(14)00062-0. PMID: 24576618.

DRSC DIOPT and DIOPT-DIST ortholog tools now include Xenopus and S. pombe

The DRSC is pleased to announce that our DIOPT and DIOPT-DIST tools for ortholog search now include Xenopus and S. pombe in addition to fly, worm, S. cerevisiae, zebrafish, mouse and human. We added these two new species in response to community feedback.

What's the difference between DIOPT and DIOPT-DIST?

DIOPT lets you search for orthologs for any pair of species (e.g. zebrafish orthologs of fly genes, or yeast orthologs of a mouse gene). Results from 10 different public tools/alorithms are shown.

DIOPT-DIST lets you search using any of the non-human species we report, and view not just putative human orthologs but also connections between those human orthologs and disease. Alternatively, you can start with a disease, view human genes associated with that disease and orthologs of those human genes in a given species of interest.

If you use these tools, please cite our paper:  Hu et al. BMC Bioinformatics. PMID: 21880147

UP-TORR. A new tool from the DRSC. Find RNAi reagents--using today's information!

The DRSC has launched a new tool! 

And a corresponding paper is now out in the journal Genetics.

Hu Y, Roesel C, Flockhart I, Perkins L, Perrimon N, Mohr S. UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents. Genetics. 2013 Jun 21. PMID: 23792952.

UP-TORR, named for "Updated Targets of RNAi Reagents" checks daily for new updates to fly gene annotations and RNAi reagent collections (including TRiP, NIG-Japan and VDRC RNAi fly stocks). This lets you view the most updated interpretation of the gene-to-RNAi-reagent relationship.

Why does this matter? Because gene annotations change--sometimes a lot--over time, changing the interpretation of on-targets and off-targets of a reagent.

Please check out our paper to learn more. We also have a help page and a video demo online. As always, feedback on the online tool is welcome.

COMPLEAT complex enrichment tool

The DRSC is pleased to announce that we are making COMPLEAT available in our suite of online software tools.

Conceptually similar to gene set enrichment, COMPLEAT makes it possible to look for enrichment of predicted protein complexes in a large-scale RNAi data set--including those with multiple conditions or time-points. You'll see a graph (left-hand side) and can click do draw a polygon around points on the graph to view those specific complexes (right-hand side).

The online tool web pages include a Demo (narrated video) and a set of Example Files so you can test out the tool and see the data upload format. As always, your feedback is welcome!

Here's the citation and abstract from the paper, as well as a screenshot.

Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N. Protein complex-based analysis framework for high-throughput data sets.  Sci Signal. 2013 Feb 26;6(264):rs5. PMID: 23443684

Abstract: Analysis of high-throughput data increasingly relies on pathway annotation and functional information derived from Gene Ontology. This approach has limitations, in particular for the analysis of network dynamics over time or under different experimental conditions, in which modules within a network rather than complete pathways might respond and change. We report an analysis framework based on protein complexes, which are at the core of network reorganization. We generated a protein complex resource for human, Drosophila, and yeast from the literature and databases of protein-protein interaction networks, with each species having thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat), a tool for data mining and visualization for complex-based analysis of high-throughput data sets, as well as analysis and integration of heterogeneous proteomics and gene expression data sets. With COMPLEAT, we identified dynamically regulated protein complexes among genome-wide RNA interference data sets that used the abundance of phosphorylated extracellular signal-regulated kinase in cells stimulated with either insulin or epidermal growth factor as the output. The analysis predicted that the Brahma complex participated in the insulin response.

Ranking the Rankings. Breaking report.

On my desk to read today--this report of comparison among large-scale screen ranking methods and development of a new approach.

Siebourg J, Merdes G, Misselwitz B, Hardt WD, Beerenwinkel N. Stability of gene rankings from RNAi screens. Bioinformatics. 28(12):1612-8. PMID: 22513992.