Monday, July 28, 2014

Genome-wide, high-content image-based screen preformed at DRSC--identification of regulators of organization of polycomb foci

Gonzalez I, Mateos-Langerak J, Thomas A, Cheutin T, Cavalli G. Identification of regulators of the three-dimensional polycomb organization by a microscopy-based genome-wide RNAi screen. Mol Cell. 2014 May 8;54(3):485-99. PMID: 24703951.  

From the abstract: "... Here, we report the results of a high-resolution microscopy genome-wide RNAi screen that identifies 129 genes that regulate the nuclear organization of Pc foci. Candidate genes include PcG components and chromatin factors, as well as many protein-modifying enzymes, including components of the SUMOylation pathway. ... suggesting that the dynamic regulation of Pc SUMOylation regulates PcG-mediated silencing by modulating the kinetics of Pc binding to chromatin as well as its ability to form Polycomb foci."

Thursday, July 24, 2014

Cell-based assays related to Notch signaling

Xu A, Irvine KD. Notch-ligand binding assays in Drosophila cells. Methods Mol Biol. 2014;1187:277-84. PMID: 25053497.

 Li J, Housden BE, Bray SJ. Notch signaling assays in Drosophila cultured cell lines. Methods Mol Biol. 2014;1187:131-41. PMID: 25053486.

Monday, July 21, 2014

RNA biology--viruses & RNAi suppression

van Mierlo JT, Overheul GJ, Obadia B, van Cleef KW, Webster CL, Saleh MC, Obbard DJ, van Rij RP. Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi. PLoS Pathog. 2014 Jul 7;10(7):e1004256. PMID: 25032815.

Genetic manipulation of both host cells and pathogen--"iMAD" protocol

O'Connor TJ, Isberg RR. iMAD, a genetic screening strategy for dissecting complex interactions between a pathogen and its host. Nat Protoc. 2014 Aug;9(8):1916-30. PMID: 25033208.

From the abstract: "... Here we present a protocol for dissecting the interaction between a pathogen (Legionella pneumophila) and its host (cultured Drosophila melanogaster cells) using bacterial mutagenesis and host RNAi. ..."

Sunday, July 20, 2014

Genome-wide RNAi screen identifies neurons involved in female receptivity behavior

Bussell JJ, Yapici N, Zhang SX, Dickson BJ, Vosshall LB. Abdominal-B Neurons Control Drosophila Virgin Female Receptivity. Curr Biol. 2014 Jul 3. pii: S0960-9822(14)00689-7. PMID: 24998527.

From the abstract: "... Using a genome-wide neuronal RNAi screen, we identify a subpopulation of neurons responsible for pausing, a novel behavioral aspect of virgin female receptivity characterized in this study. ..."

in vivo RNAi screen related to Notch signaling in follicle cells

Xie G, Yu Z, Jia D, Jiao R, Deng WM. E(y)1/TAF9 mediates the transcriptional output of Notch signaling in Drosophila. J Cell Sci. 2014 Jul 11. PMID: 25015288.

From the abstract: "... We identified E(y)1/TAF9 in a large-scale in vivo RNAi screen for genes involved in a Notch-dependent mitotic-to-endocycle transition in Drosophila follicle cells. Knockdown of e(y)1/TAF9 displayed Notch-like phenotypes ..."

Fly RNAi screen of about 150 genes included in obesity study

Lee JH, Bassel-Duby R, Olson EN. Heart- and muscle-derived signaling system dependent on MED13 and Wingless controls obesity in Drosophila. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9491-6. PMID: 24979807.

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."

Wing blisters as model for tissue morphogenesis--in vivo RNAi study

Bilousov O, Koval A, Keshelava A, Katanaev VL. Identification of novel elements of the Drosophila blisterome sheds light on potential pathological mechanisms of several human diseases. PLoS One. 2014 Jun 26;9(6):e101133. PMID: 24968325; PMCID: PMC4072764. From the abstract: "... Here we focused on Drosophila wing tissue morphogenesis, a fairly complex developmental program ... By means of RNAi-silencing technique and the blister phenotype as readout, we identify numerous novel proteins potentially involved in wing sheet adhesion ..."

in vivo fly RNAi screen looks at cytoskeletal and other components in muscle

Perkins AD, Tanentzapf G. An Ongoing Role for Structural Sarcomeric Components in Maintaining Drosophila melanogaster Muscle Function and Structure. PLoS One. 2014 Jun 10;9(6):e99362. PMID: 24915196; PMCID: PMC4051695.

in vivo fly RNAi kinase and phosphatase screen looks at synapse

Bulat V, Rast M, Pielage J. Presynaptic CK2 promotes synapse organization and stability by targeting Ankyrin2. J Cell Biol. 2014 Jan 6;204(1):77-94. PMID: 24395637; PMCID: PMC3882785.

in vivo RNAi screen related to cell death points to CDK7

Morishita J, Kang MJ, Fidelin K, Ryoo HD. CDK7 regulates the mitochondrial localization of a tail-anchored proapoptotic protein, Hid. Cell Rep. 2013 Dec 26;5(6):1481-8. PMID: 24360962; PMCID: PMC3892150.

Running oranelles on an S2 cell track (with or without RNAi treatment)

Lu W, Del Castillo U, Gelfand VI. Organelle transport in cultured Drosophila cells: S2 cell line and primary neurons. J Vis Exp. 2013 Nov 20;(81):e50838. PMID: 24300413.

Biology of the RNAi pathway--Argonaute-mediated microRNA biogenesis

Yang JS, Smibert P, Westholm JO, Jee D, Maurin T, Lai EC. Intertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila. Nucleic Acids Res. 2014 Feb;42(3):1987-2002. PMID: 24220090; PMCID: PMC3919586.  

From the abstract: "Although Dicer is essential for general microRNA (miRNA) biogenesis, vertebrate mir-451 is Dicer independent. Instead, its short pre-miRNA hairpin is 'sliced' by Ago2, then 3'-resected into mature miRNAs. Here, we show that Drosophila cells and animals generate functional small RNAs from mir-451-type precursors. ... Altogether, we document unexpected aspects of miRNA biogenesis and Ago sorting, and provide insights into maturation of Argonaute-cleaved miRNA substrates."

Follow-up on RNAi screen links SCF(Skp2) and Double-parked

Kroeger PT Jr, Shoue DA, Mezzacappa FM, Gerlach GF, Wingert RA, Schulz RA. Knockdown of SCF(Skp2) function causes double-parked accumulation in the nucleus and DNA re-replication in Drosophila plasmatocytes. PLoS One. 2013 Oct 24;8(10):e79019. PMID: 24205363; PMCID: PMC3812016.

RNAi targeting of 270 fly orthologs of human genes helps reveal conserved functional networks related to intellectual disability

See this post in Drosophila Models of Human Disease.

Wednesday, July 9, 2014

New fly CRISPR report

Fillip Port (a past DRSC screener) and colleagues have published a new report on CRISPRs in flies. Additional data included as compared with their online preprint.

Port F, Chen HM, Lee T, Bullock SL. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc Natl Acad Sci U S A. 2014 Jul 7. pii: 201405500. PMID: 25002478.