Review Article

2016
Housden BE, Perrimon N. Design and Generation of Donor Constructs for Genome Engineering in Drosophila. Cold Spring Harb Protoc. 2016;2016 (9) :pdb.prot090787. Abstract

The generation of precise alterations to the genome using CRISPR requires the combination of CRISPR and a donor construct containing homology to the target site. A double-strand break is first generated at the target locus using CRISPR. It is then repaired using the endogenous homologous recombination (HR) pathway. When a donor construct is provided, it can be used as a template for HR repair and can therefore be exploited to introduce alterations in the genomic sequence with single base-pair precision. Here we describe a protocol for the generation of donor constructs using Golden Gate assembly and discuss some key considerations for donor construct design for use in Drosophila.

2016_CSHP_Housden_DonorConstructs.pdf
Housden BE, Hu Y, Perrimon N. Design and Generation of Drosophila Single Guide RNA Expression Constructs. Cold Spring Harb Protoc. 2016;2016 (9) :pdb.prot090779. Abstract

The recent advances in CRISPR-based genome engineering have enabled a plethora of new experiments to study a wide range of biological questions. The major attraction of this system over previous methods is its high efficiency and simplicity of use. For example, whereas previous genome engineering technologies required the generation of new proteins to target each new locus, CRISPR requires only the expression of a different single guide RNA (sgRNA). This sgRNA binds to the Cas9 endonuclease protein and directs the generation of a double-strand break to a highly specific genomic site determined by the sgRNA sequence. In addition, the relative simplicity of the Drosophila genome is a particular advantage, as possible sgRNA off-target sites can easily be avoided. Here, we provide a step-by-step protocol for designing sgRNA target sites using the Drosophila RNAi Screening Center (DRSC) Find CRISPRs tool (version 2). We also describe the generation of sgRNA expression plasmids for the use in cultured Drosophila cells or in vivo. Finally, we discuss specific design requirements for various genome engineering applications.

2016_CSHP_Housden_SingleGuideRNA.pdf
Housden BE, Perrimon N. Detection of Indel Mutations in Drosophila by High-Resolution Melt Analysis (HRMA). Cold Spring Harb Protoc. 2016;2016 (9) :pdb.prot090795. Abstract

Although CRISPR technology allows specific genome alterations to be created with relative ease, detection of these events can be problematic. For example, CRISPR-induced double-strand breaks are often repaired imprecisely to generate unpredictable short indel mutations. Detection of these events requires the use of molecular screening techniques such as endonuclease assays, restriction profiling, or high-resolution melt analysis (HRMA). Here, we provide detailed protocols for HRMA-based mutation screening in Drosophila and analysis of the resulting data using the online tool HRMAnalyzer.

2016_CSHP_Housden_HRMA.pdf
Sahin M, Henske EP, Manning BD, Ess KC, Bissler JJ, Klann E, et al. Advances and Future Directions for Tuberous Sclerosis Complex Research: Recommendations From the 2015 Strategic Planning Conference. Pediatr Neurol. 2016;60 :1-12. Abstract

On March 10 to March 12, 2015, the National Institute of Neurological Disorders and Stroke and the Tuberous Sclerosis Alliance sponsored a workshop in Bethesda, Maryland, to assess progress and new opportunities for research in tuberous sclerosis complex with the goal of updating the 2003 Research Plan for Tuberous Sclerosis (http://www.ninds.nih.gov/about_ninds/plans/tscler_research_plan.htm). In addition to the National Institute of Neurological Disorders and Stroke and Tuberous Sclerosis Alliance, participants in the strategic planning effort and workshop included representatives from six other Institutes of the National Institutes of Health, the Department of Defense Tuberous Sclerosis Complex Research Program, and a broad cross-section of basic scientists and clinicians with expertise in tuberous sclerosis complex along with representatives from the pharmaceutical industry. Here we summarize the outcomes from the extensive premeeting deliberations and final workshop recommendations, including (1) progress in the field since publication of the initial 2003 research plan for tuberous sclerosis complex, (2) the key gaps, needs, and challenges that hinder progress in tuberous sclerosis complex research, and (3) a new set of research priorities along with specific recommendations for addressing the major challenges in each priority area. The new research plan is organized around both short-term and long-term goals with the expectation that progress toward specific objectives can be achieved within a five to ten year time frame.

2016_Pediatr Neurol_Sahin.pdf Appendices.zip
Housden BE, Perrimon N. Comparing CRISPR and RNAi-based screening technologies. Nat Biotechnol. 2016;34 (6) :621-3. 2016_Nat Biotech_Housden.pdf
Petsakou A, Perrimon N. "ISN't Thirst Sweet?" Says the Fly. Cell. 2016;166 (4) :796-7. Abstract

How food and water intake is reciprocally regulated to maintain homeostasis is unclear. New findings by Jourjine and colleagues identify four neurons in the Drosophila brain that receive both water and sugar abundance signals and oppositely regulate hunger and thirst.

2016_Cell_Petsakou.pdf
Mohr SE, Hu Y, Ewen-Campen B, Housden BE, Viswanatha R, Perrimon N. CRISPR guide RNA design for research applications. FEBS J. 2016;Abstract

The rapid rise of CRISPR as a technology for genome engineering and related research applications has created a need for algorithms and associated online tools that facilitate design of on-target and effective guide RNAs (gRNAs). Here, we review the state-of-the-art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, including knockout, activation and inhibition. Notably, achieving good gRNA design is not solely dependent on innovations in CRISPR technology. Good design and design tools also rely on availability of high-quality genome sequence and gene annotations, as well as on availability of accumulated data regarding off-targets and effectiveness metrics. This article is protected by copyright. All rights reserved.

2016_FEBS_Mohr.pdf
2015
Owusu-Ansah E, Perrimon N. Stress signaling between organs in metazoa. Annu Rev Cell Dev Biol. 2015;31 :497-522. Abstract

Many organisms have developed a robust ability to adapt and survive in the face of environmental perturbations that threaten the integrity of their genome, proteome, or metabolome. Studies in multiple model organisms have shown that, in general, when exposed to stress, cells activate a complex prosurvival signaling network that includes immune and DNA damage response genes, chaperones, antioxidant enzymes, structural proteins, metabolic enzymes, and noncoding RNAs. The manner of activation runs the gamut from transcriptional induction of genes to increased stability of transcripts to posttranslational modification of important biosynthetic proteins within the stressed tissue. Superimposed on these largely autonomous effects are nonautonomous responses in which the stressed tissue secretes peptides and other factors that stimulate tissues in different organs to embark on processes that ultimately help the organism as a whole cope with stress. This review focuses on the mechanisms by which tissues in one organ adapt to environmental challenges by regulating stress responses in tissues of different organs.

2015_Annu Rev Cell Dev_Owusu.pdf
2014
Tipping M, Perrimon N. Drosophila as a model for context-dependent tumorigenesis. J Cell Physiol. 2014;229 (1) :27-33. Abstract

Drosophila can exhibit classic hallmarks of cancer, such as evasion of apoptosis, sustained proliferation, metastasis, prolonged survival, genome instability, and metabolic reprogramming, when cancer-related genes are perturbed. In the last two decades, studies in flies have identified several tumor suppressor and oncogenes. However, the greatest strength of the fly lies in its ability to model cancer hallmarks in a variety of tissue types, which enables the study of context-dependent tumorigenesis. We review the organs and tissues that have been used to model tumor formation, and propose new strategies to maximize the potential of Drosophila in cancer research.

2014_J Cell Phys_Tipping.pdf
Zhou R, Mohr S, Hannon GJ, Perrimon N. Inducing RNAi in Drosophila cells by soaking with dsRNA. Cold Spring Harb Protoc. 2014;2014 (5). Abstract

RNA interference (RNAi) triggered by synthetic long double-stranded RNAs (dsRNAs) has been applied in many Drosophila cell lines to study the functions of individual genes or for genome-wide scans. One contributor to the popularity of this approach is that many fly cell lines spontaneously take up dsRNAs from media, obviating the need for assisted uptake methods such as transfection. In this protocol, RNAi is induced in Drosophila S2 cells by soaking with dsRNA. Cell lines other than S2 can also be used, although the ability of each line to passively take up dsRNA does vary. Therefore, the efficiency of passive uptake should be carefully verified for each line.

2014_CSH Perspect_Zhou.pdf
Piccirillo R, Demontis F, Perrimon N, Goldberg AL. Mechanisms of muscle growth and atrophy in mammals and Drosophila. Dev Dyn. 2014;243 (2) :201-15. Abstract

BACKGROUND: The loss of skeletal muscle mass (atrophy) that accompanies disuse and systemic diseases is highly debilitating. Although the pathogenesis of this condition has been primarily studied in mammals, Drosophila is emerging as an attractive system to investigate some of the mechanisms involved in muscle growth and atrophy. RESULTS: In this review, we highlight the outstanding unsolved questions that may benefit from a combination of studies in both flies and mammals. In particular, we discuss how different environmental stimuli and signaling pathways influence muscle mass and strength and how a variety of disease states can cause muscle wasting. CONCLUSIONS: Studies in Drosophila and mammals should help identify molecular targets for the treatment of muscle wasting in humans.

2014_Dev Dyn_Piccirillo.pdf
Owusu-Ansah E, Perrimon N. Modeling metabolic homeostasis and nutrient sensing in Drosophila: implications for aging and metabolic diseases. Dis Model Mech. 2014;7 (3) :343-50. Abstract

Over the past decade, numerous reports have underscored the similarities between the metabolism of Drosophila and vertebrates, with the identification of evolutionarily conserved enzymes and analogous organs that regulate carbohydrate and lipid metabolism. It is now well established that the major metabolic, energy-sensing and endocrine signaling networks of vertebrate systems are also conserved in flies. Accordingly, studies in Drosophila are beginning to unravel how perturbed energy balance impinges on lifespan and on the ensuing diseases when energy homeostasis goes awry. Here, we highlight several emerging concepts that are at the nexus between obesity, nutrient sensing, metabolic homeostasis and aging. Specifically, we summarize the endocrine mechanisms that regulate carbohydrate and lipid metabolism, and provide an overview of the neuropeptides that regulate feeding behavior. We further describe the various efforts at modeling the effects of high-fat or -sugar diets in Drosophila and the signaling mechanisms involved in integrating organ function. Finally, we draw attention to some of the cardinal discoveries made with these disease models and how these could spur new research questions in vertebrate systems.

2014_DMM_Owusu-Ansah.pdf
Mohr SE, Hu Y, Kim K, Housden BE, Perrimon N. Resources for functional genomics studies in Drosophila melanogaster. Genetics. 2014;197 (1) :1-18. Abstract

Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, "meta" information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.

2014_Genetics_Mohr.pdf
Mohr SE, Smith JA, Shamu CE, Neumüller RA, Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol. 2014;15 (9) :591-600. Abstract

Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks.

2014_Nat Rev MCB_Mohr.pdf
Droujinine IA, Yan D, Perrimon N. A sharp end to sugary Wingless travels. J Cell Biol. 2014;206 (7) :819-21. Abstract

Drosophila melanogaster follicle stem cells are controlled by Wingless (Wg) ligands secreted 50 µm away, raising the question of how long-distance Wg spreading occurs. In this issue of JCB, Wang and Page-McCaw (2014. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201403084) demonstrate a potential mechanism by which the heparan sulfate proteoglycan Dally-like (Dlp) promotes Wg travel, whereas matrix Mmp2 (Metalloproteinase 2) impedes it by inactivating Dlp.

2014_JCB_Droujinine.pdf
Housden BE, Perrimon N. Spatial and temporal organization of signaling pathways. Trends Biochem Sci. 2014;39 (10) :457-64. Abstract

The development and maintenance of the many different cell types in metazoan organisms requires robust and diverse intercellular communication mechanisms. Relatively few such signaling pathways have been identified, leading to the question of how such a broad diversity of output is generated from relatively simple signals. Recent studies have revealed complex mechanisms integrating temporal and spatial information to generate diversity in signaling pathway output. We review some general principles of signaling pathways, focusing on transcriptional outputs in Drosophila. We consider the role of spatial and temporal aspects of different transduction pathways and then discuss how recently developed tools and approaches are helping to dissect the complex mechanisms linking pathway stimulation to output.

2014_Trends Bio Sci_Housden.pdf
Doupé DP, Perrimon N. Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. Sci Signal. 2014;7 (319) :re1. Abstract

The use of genome-wide proteomic and RNA interference approaches has moved our understanding of signal transduction from linear pathways to highly integrated networks centered on core nodes. However, probing the dynamics of flow of information through such networks remains technically challenging. In particular, how the temporal dynamics of an individual pathway can elicit distinct outcomes in a single cell type and how multiple pathways may interact sequentially or synchronously to influence cell fate remain open questions in many contexts. The development of fluorescence-based reporters and optogenetic regulators of pathway activity enables the analysis of signaling in living cells and organisms with unprecedented spatiotemporal resolution and holds the promise of addressing these key questions. We present a brief overview of the evidence for the importance of temporal dynamics in cellular regulation, introduce these fluorescence-based tools, and highlight specific studies that leveraged these tools to probe the dynamics of information flow through signaling networks. In particular, we highlight two studies in Caenorhabditis elegans sensory neurons and cultured mammalian cells that demonstrate the importance of signal dynamics in determining cellular responses.

2014_Sci Sig_Doupe.pdf
2013
Demontis F, Piccirillo R, Goldberg AL, Perrimon N. Mechanisms of skeletal muscle aging: insights from Drosophila and mammalian models. Dis Model Mech. 2013;6 (6) :1339-52. Abstract

A characteristic feature of aged humans and other mammals is the debilitating, progressive loss of skeletal muscle function and mass that is known as sarcopenia. Age-related muscle dysfunction occurs to an even greater extent during the relatively short lifespan of the fruit fly Drosophila melanogaster. Studies in model organisms indicate that sarcopenia is driven by a combination of muscle tissue extrinsic and intrinsic factors, and that it fundamentally differs from the rapid atrophy of muscles observed following disuse and fasting. Extrinsic changes in innervation, stem cell function and endocrine regulation of muscle homeostasis contribute to muscle aging. In addition, organelle dysfunction and compromised protein homeostasis are among the primary intrinsic causes. Some of these age-related changes can in turn contribute to the induction of compensatory stress responses that have a protective role during muscle aging. In this Review, we outline how studies in Drosophila and mammalian model organisms can each provide distinct advantages to facilitate the understanding of this complex multifactorial condition and how they can be used to identify suitable therapies.

2013_Dis Mod Mech_Demontis.pdf
Droujinine IA, Perrimon N. Defining the interorgan communication network: Systemic coordination of organismal cellular processes under homeostasis and localized stress. Frontiers in Cellular and Infection Microbiology . 2013;3 (82) :1-5. 2013_FCMB_Droujinine.pdf
Zhou R, Mohr S, Hannon GJ, Perrimon N. Inducing RNAi in Drosophila cells by transfection with dsRNA. Cold Spring Harb Protoc. 2013;2013 (5) :461-3. Abstract

In Drosophila cells, RNA interference (RNAi) can be triggered by synthetic long double-stranded RNAs (dsRNAs). For many Drosophila cell lines and cell types, passive dsRNA uptake is inefficient. More complete silencing responses can often be obtained in Drosophila S2 cells using transfection, perhaps because higher levels of intracellular dsRNA are achieved. In this protocol, S2 cells are transfected with dsRNA using QIAGEN's Effectene reagent, which has proven to be reliable for many investigators. A plasmid DNA can also be included in the transfection mix to provide additional functionality. The plasmid DNA can encode, for example, a reporter of the activity of a pathway or specific transcription factor, or a marker that allows visualization of some cellular behavior or structure. It is also useful to include a plasmid that encodes a fluorescent protein simply to monitor transfection efficiency.

2013_CSH Perspect_Zhou.pdf

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