Perrimon N et al. (2010) Cold Spring Harb Perspect Biol "In vivo RNAi: today and tomorrow."

Perrimon N, Perkins L, Ni JQ

[Cold Spring Harb Perspect Biol, 2010]

RNA interference (RNAi) provides a powerful reverse genetics approach to analyze gene functions both in tissue culture and in vivo. Because of its widespread applicability and effectiveness it has become an essential part of the tool box kits of model organisms such as Caenorhabditis elegans, Drosophila, and the mouse. In addition, the use of RNAi in animals in which genetic tools are either poorly developed or nonexistent enables a myriad of fundamental questions to be asked. Here, we review the methods and applications of in vivo RNAi to characterize gene functions in model organisms and discuss their impact to the study of developmental as well as evolutionary questions. Further, we discuss the applications of RNAi technologies to crop improvement, pest control and RNAi therapeutics, thus providing an appreciation of the potential for phenomenal applications of RNAi to agriculture and medicine.

Duffy JB et al. (1996) Curr Opin Cell Biol "Recent advances in understanding signal transduction pathways in worms and flies."

Duffy JB, Perrimon N

[Curr Opin Cell Biol, 1996]

One major challenge in the fields of signal transduction and pattern formation is to understand how multiple signals are integrated to determine cell fates. Two developmental systems, vulval development in Caenorhabditis elegans and axis formation during Drosophila melanogaster oogenesis, require the epidermal growth factor receptor tyrosine kinase and the NOTCH signaling pathways to specify cell fates. Current work in both systems has provided new opportunities to investigate the potential for the cross-talk between these different signaling pathways.

Mohr SE et al. (2011) Wiley Interdiscip Rev RNA "RNAi screening: new approaches, understandings, and organisms."

Mohr SE, Perrimon N

[Wiley Interdiscip Rev RNA, 2011]

RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.

Doupe DP et al. (2014) Sci Signal "Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools."

Perrimon N, Doupe DP

[Sci Signal, 2014]

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.

Moon RT et al. (2002) Science "The promise and perils of Wnt signaling through beta-catenin."

Boutros M, Moon RT, Perrimon N, Bowerman B

[Science, 2002]

Wnt pathways are involved in the control of gene expression, cell behavior, cell adhesion, and cell polarity. In addition, they often operate in combination with other signaling pathways. The Wnt/beta-catenin pathway is the best studied of the Wnt pathways and is highly conserved through evolution. In this pathway, Wnt signaling inhibits the degradation of beta-catenin, which can regulate transcription of a number of genes. Some of the genes regulated are those associated with cancer and other diseases (for example, colorectal cancer and melanomas). As a result, components of the Wnt/beta-catenin pathway are promising targets in the search for therapeutic agents. Information about Wnt pathways is available both in canonical terms and at the species level. In addition to the canonical Wnt/beta-catenin pathway, information is now available for Drosophila, Caenorhabditis elegans, and Xenopus. The STKE Connections Maps for these pathways provide an important tool in accessing this large body of complex information.

Nagy A et al. (2003) Nat Genet "Tailoring the genome: the power of genetic approaches."

Sandmeyer S, Nagy A, Perrimon N, Plasterk R

[Nat Genet, 2003]

In the last century, genetics has developed into one of the most powerful tools for addressing basic questions concerning inheritance, development, individual and social operations and death. Here we summarize the current approaches to these questions in four of the most advanced models organisms: Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly) and Mus musculus (mouse). The genomes of each of these four models have been sequenced, and all have well developed methods of efficient genetic manipulations.

Schachter H (2009) Carbohydr Res "Paucimannose N-glycans in Caenorhabditis elegans and Drosophila melanogaster."

Schachter H

[Carbohydr Res, 2009]

There is a rich diversity of paucimannose N-glycans in worms and flies, and these may play a role in the survival of these organisms. Although paucimannose N-glycans are not expressed in vertebrates, complex N-glycans may take over some of the functions of paucimannose N-glycans. Identification of the target proteins of beta-1,2-N-acetylglucosaminyltransferase I (GnTI) in worms and flies and elucidation of their functions may thus lead to a better understanding of the role of GnTI-dependent glycoproteins in the survival/longevity of both invertebrates and vertebrates.

Parkhitko AA et al. (2020) Ageing Res Rev "Targeting metabolic pathways for extension of lifespan and healthspan across multiple species."

Moskalev A, Filine E, Perrimon N, Mohr SE, Parkhitko AA

[Ageing Res Rev, 2020]

Metabolism plays a significant role in the regulation of aging at different levels, and metabolic reprogramming represents a major driving force in aging. Metabolic reprogramming leads to impaired organismal fitness, an age-dependent increase in susceptibility to diseases, decreased ability to mount a stress response, and increased frailty. The complexity of age-dependent metabolic reprogramming comes from the multitude of levels on which metabolic changes can be connected to aging and regulation of lifespan. This is further complicated by the different metabolic requirements of various tissues, cross-organ communication via metabolite secretion, and direct effects of metabolites on epigenetic state and redox regulation; however, not all of these changes are causative to aging. Studies in yeast, flies, worms, and mice have played a crucial role in identifying mechanistic links between observed changes in various metabolic traits and their effects on lifespan. Here, we review how changes in the organismal and organ-specific metabolome are associated with aging and how targeting of any one of over a hundred different targets in specific metabolic pathways can extend lifespan. An important corollary is that restriction or supplementation of different metabolites can change activity of these metabolic pathways in ways that improve healthspan and extend lifespan in different organisms. Due to the high levels of conservation of metabolism in general, translating findings from model systems to human beings will allow for the development of effective strategies for human health- and lifespan extension.

Schachter H (2009) Trends Glycosci Glycotechnol "The functions of paucimannose N-glycans in Caenorhabditis elegans"

Schachter H

[Trends Glycosci Glycotechnol, 2009]

Caenorhabditis elegans makes about 150 individual N-glycan structures. This review discusses the synthesis and possible functions of the paucimannose N-glycans that are highly abundant in invertebrates but not in vertebrates. The complexity of the worm's N-glycans is due in part to a variety of unusual fucosylation reactions and the addition of phosphorylcholine. Phosphorylcholine has been recognized as a widespread antigenic determinant in many important disease-causing parasites. The synthesis of paucimannose N-glycans depends on the prior action of UDP-GlcNAc:alpha 3-D-mannoside beta 1,2-N-acetylglucosaminyltransferase I (GnTI, encoded by Mgat1). There are three GnTI isoenzymes in the worm (GLY-12, GLY-13, GLY-14). Each GnTI isoenzyme has a distinct set of target proteins and a distinct role in the interaction of C.elegans with pathogenic bacteria. Identification of the protein substrates of GnTI in worms and elucidation of their functions may lead to a better understanding of the role of GnTI-dependent glycoproteins in the survival of both invertebrates and vertebrates.

Polevoda B et al. (2003) J Mol Biol "N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins."

Polevoda B, Sherman F

[J Mol Biol, 2003]

N(alpha)-terminal acetylation occurs in the yeast Saccharomyces cerevisiae by any of three N-terminal acetyltransferases (NAT), NatA, NatB, and NatC, which contain Ard1p, Nat3p and Mak3p catalytic subunits, respectively. The N-terminal sequences required for N-terminal acetylation, i.e. the NatA, NatB, and NatC substrates, were evaluated by considering over 450 yeast proteins previously examined in numerous studies, and were compared to the N-terminal sequences of more than 300 acetylated mammalian proteins. In addition, acetylated sequences of eukaryotic proteins were compared to the N termini of 810 eubacterial and 175 archaeal proteins, which are rarely acetylated. Protein orthologs of Ard1p, Nat3p and Mak3p were identified with the eukaryotic genomes of the sequences of model organisms, including Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Mus musculus and Homo sapiens. Those and other putative acetyltransferases were assigned by phylogenetic analysis to the following six protein families: Ard1p; Nat3p; Mak3p; CAM; BAA; and Nat5p. The first three families correspond to the catalytic subunits of three major yeast NATs; these orthologous proteins were identified in eukaryotes, but not in prokaryotes; the CAM family include mammalian orthologs of the recently described Camello1 and Camello2 proteins whose substrates are unknown; the BAA family comprise bacterial and archaeal putative acetyltransferases whose biochemical activity have not been characterized; and the new Nat5p family assignment was on the basis of putative yeast NAT, Nat5p (YOR253W). Overall patterns of N-terminal acetylated proteins and the orthologous genes possibly encoding NATs suggest that yeast and higher eukaryotes have the same systems for N-terminal acetylation.