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RNAi for Plant Functional Genomics

Louisa Matthew
2004 Comparative and Functional Genomics  
A major challenge in the post-genome era of plant biology is to determine the functions of all the genes in the plant genome.  ...  RNAi has been used very effectively inCaenorhabditis elegansfunctional genomics, and resources are currently being developed for the application of RNAi to high-throughput plant functional genomics.  ...  By screening for T-DNA and transposon insertions in 73 of these genes, 47 insertions in 36 different target genes were identified [30] .  ... 
doi:10.1002/cfg.396 pmid:18629158 pmcid:PMC2447448 fatcat:uetfsjpihrbvnn6ea5m4iff7pu

RNAi: Applications in Vertebrate Pest Management

Katherine E. Horak
2020 Trends in Biotechnology  
Sequence-directed inhibition of protein synthesis by RNAi has potential as a means to control pest wildlife. Species specific by design, RNAi reduces impacts on nontarget species and the environment.  ...  Additional research advancing the field of RNAi-based management of vertebrate pest wildlife is timely.  ...  The silencing of genes using RNAi can be more cost-effective and humane with fewer nontarget effects than current approaches.  ... 
doi:10.1016/j.tibtech.2020.05.001 pmid:32466968 fatcat:mnlyhhnwbjb7nl3xdnyiy4ncqu

Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila

Ralph A. Neumüller, Norbert Perrimon
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Through the creation of tools for both, in vitro and in vivo genomewide RNAi screens, Drosophila melanogaster has emerged as one of the key model organisms in systems biology research and over the last  ...  In particular, RNA interference (RNAi)-based highthroughput screens have been instrumental in determining the composition of regulatory systems and paired with integrative data analyses have begun to delineate  ...  ACKNOWLEDGEMENTS We would like to thank the members of the Perrimon laboratory for discussions and Richelle Sopko for critically reading the manuscript.  ... 
doi:10.1002/wsbm.127 pmid:21197652 pmcid:PMC3560415 fatcat:n7pqximbwnatvnvtetd53u52fa

Cellular phenotyping by RNAi

F. Fuchs
2006 Briefings in Functional Genomics & Proteomics  
A systematic characterization of genes with unknown function is a key challenge after the sequencing of the human genome and the genomes of many model organisms.  ...  In addition, progress in screening technologies and data analysis allows the adaptation of screening methods to analyse more complex cellular processes.  ...  These approaches have been effectively used to study many different biological pathways in loss-of-function analysis, and several large-scale efforts have recently generated libraries that target every  ... 
doi:10.1093/bfgp/ell007 pmid:16769679 fatcat:7qpz2zzsizck3f6bnipm7rstki

Discovery of Novel Targets with High Throughput RNA Interference Screening

Paul Kassner
2008 Combinatorial chemistry & high throughput screening  
However, these approaches usually require painstaking in silico analysis and low-throughput basic wet-lab research to identify the function of a gene and validate the gene product as a potential therapeutic  ...  With a carefully chosen phenotype, an understanding of the biology of RNAi and appreciation of the limitations of RNAi screening, there is great potential for the discovery of new drug targets.  ...  INTRODUCTION RNA Interference The identification of RNA interference (RNAi) in C. elegans [1] initiated a large research effort to define the biological role and mechanism of action of RNAi.  ... 
doi:10.2174/138620708783877744 pmid:18336211 fatcat:52vwt2xx4nb67nxr3y7obpyqhq

Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target

Julia Ulrich, Van Anh Dao, Upalparna Majumdar, Christian Schmitt-Engel, Jonas Schwirz, Dorothea Schultheis, Nadi Ströhlein, Nicole Troelenberg, Daniela Grossmann, Tobias Richter, Jürgen Dönitz, Lizzy Gerischer (+4 others)
2015 BMC Genomics  
Conclusions: Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target  ...  From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets.  ...  Acknowledgments We acknowledge support by the German Research Foundation (DFG), which funded the iBeetle project (FOR1234) but was not involved in design or analysis of the data or its publication.  ... 
doi:10.1186/s12864-015-1880-y pmid:26334912 pmcid:PMC4559001 fatcat:4qj75trv2vdf7g5v2jusnydt24

RNAi targeting Caenorhabditis elegans α-arrestins has little effect on lifespan

Sangsoon Park, Yoonji Jung, Seon Woo A. An, Heehwa G. Son, Wooseon Hwang, Dongyeop Lee, Murat Artan, Hae-Eun H. Park, Dae-Eun Jeong, Yujin Lee, Seung-Jae V. Lee
2017 F1000Research  
This study will provide useful information for future research on Conclusions: the functional role of α-arrestins in aging and longevity.  ...  Here, we sought to examine the roles of α-arrestins in the longevity Methods: of through an RNA interference screen.  ...  In the results paragraph the authors state that 'knockdown of each of individual α-arrestin genes  ... 
doi:10.12688/f1000research.12337.3 pmid:29123644 pmcid:PMC5657022 fatcat:qitsnksklrhsvf6jdhjyhfty5a

Studying gene function in Caenorhabditis elegans using RNA-mediated interference

E. M. Maine
2008 Briefings in Functional Genomics & Proteomics  
The RNA interference (RNAi) method for targeted gene silencing is widely used in Caenorhabditis elegans for largescale functional genomic studies, analysis of limited gene sets and detailed analysis of  ...  The application of RNAi has identified genes that participate in various aspects of development, physiology and cell biology.  ...  Acknowledgements The author thanks Jane Hubbard for communicating data prior to publication, and Xingyu She and two anonymous reviewers for comments on the manuscript.  ... 
doi:10.1093/bfgp/eln019 pmid:18443013 fatcat:2m6wv53p65ga7pu5m6qemm73yy

RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.)

Ibrokhim Y. Abdurakhmonov, Mirzakamol S. Ayubov, Khurshida A. Ubaydullaeva, Zabardast T. Buriev, Shukhrat E. Shermatov, Haydarali S. Ruziboev, Umid M. Shapulatov, Sukumar Saha, Mauricio Ulloa, John Z. Yu, Richard G. Percy, Eric J. Devor (+10 others)
2016 Frontiers in Plant Science  
RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic  ...  Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies,  ...  The existence and use of ARM genes in current RNAi-based cotton cultivars is subject for rising "unjustified" warnings and requests for removal of ARM genes from RNAi cultivars, and this perhaps continues  ... 
doi:10.3389/fpls.2016.00202 pmid:26941765 pmcid:PMC4762190 fatcat:ikkendqtlrdl7mcita7ekvmj7e

RNAi targeting Caenorhabditis elegans α-arrestins has small or no effects on lifespan

Sangsoon Park, Yoonji Jung, Seon Woo A. An, Heehwa G. Son, Wooseon Hwang, Dongyeop Lee, Murat Artan, Hae-Eun H. Park, Dae-Eun Jeong, Yujin Lee, Seung-Jae V. Lee
2017 F1000Research  
This study will provide useful Conclusions: information for future research on the functional role of α-arrestins in aging and longevity.  ...  Here, we sought to examine the roles of α-arrestins in the longevity Methods: of through an RNA interference screen.  ...  The authors knockdown of 24 of the 29 alpha-arrestin genes.  ... 
doi:10.12688/f1000research.12337.2 pmid:29123644 pmcid:PMC5657022 fatcat:kkvle63gnffmtgvsujkih3rcau

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

Y. Hu, C. Roesel, I. Flockhart, L. Perkins, N. Perrimon, S. E. Mohr
2013 Genetics  
and in vivo RNAi reagents.  ...  Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent-gene relationship, as well as related information regarding specificity  ...  We thank Thomas Micheler from the Vienna Drosophila RNAi Center for help with data access. We also thank all of the past and current users of the DRSC and TRiP for providing valuable feedback.  ... 
doi:10.1534/genetics.113.151340 pmid:23792952 pmcid:PMC3761311 fatcat:7q2sftjqwjhcznrimx4epf6mrm

Genome-wide RNAi

Robert Barstead
2001 Current Opinion in Chemical Biology  
Acknowledgements I wish to thank Julie Ahringer and Andrew Fire for discussions and the communication of unpublished results.  ...  In this review, I discuss recent efforts to use RNAi for largescale functional analysis of genes in C. elegans and other model systems. What is RNAi?  ...  In a typical experiment, dsRNA from a selected target gene is synthesized in vitro and injected into the germline of an adult nematode. The progeny are then examined for phenotypes.  ... 
doi:10.1016/s1367-5931(00)00173-3 pmid:11166650 fatcat:kophvlrwl5f6hhka6paryb7ide

Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis

Bahar Yilmazel, Yanhui Hu, Frederic Sigoillot, Jennifer A Smith, Caroline E Shamu, Norbert Perrimon, Stephanie E Mohr
2014 BMC Bioinformatics  
We also acknowledge NIH funding in support of the Drosophila RNAi Screening Center (R01 GM067761 to N.P.). N.P. is an Investigator of the Howard Hughes Medical Institute.  ...  Acknowledgements The authors would like to thank members of the Perrimon lab and DRSC for helpful suggestions and discussions.  ...  The user is then informed via email about the number of RNAi reagents that were ignored in the analysis and their location in the file. Output files A GESS analysis generates two output files.  ... 
doi:10.1186/1471-2105-15-192 pmid:24934636 pmcid:PMC4073188 fatcat:lxixqtv4fral7j7yg4tffuzniu

Oncology studies using siRNA libraries: the dawn of RNAi-based genomics

Christoph Sachse, Christophe J Echeverri
2004 Oncogene  
By enabling a 'clean' determination of gene function, that is the creation of direct causal links between gene and phenotype in human cells, RNAi investigations promise levels of pathophysiological relevance  ...  The available reagents and methodologies for RNAi screening studies now enable a wide range of different scopes and scales of investigation, from single-parameter assays applied to focused subsets of genes  ...  The work presented in this article has partially been supported by Grant no. 03I4002 of the German Federal Ministry of Education and Science (BMBF).  ... 
doi:10.1038/sj.onc.1208072 pmid:15517020 fatcat:64u3hlxlb5bl5l6p5jfn2aldfa

RNAi targeting Caenorhabditis elegans α-arrestins marginally affects lifespan

Sangsoon Park, Yoonji Jung, Seon Woo A. An, Heehwa G. Son, Wooseon Hwang, Dongyeop Lee, Murat Artan, Hae-Eun H. Park, Dae-Eun Jeong, Yujin Lee, Seung-Jae V. Lee
2017 F1000Research  
.: OASIS 2: online application for survival analysis 2 with features for the analysis of maximal lifespan and healthspan in aging research. Oncotarget. 2016; 7(35): 56147-56152.  ...  Kunitomo H, Uesugi H, Kohara Y, et al.: Identification of ciliated sensory neuronexpressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails. Genome Biol. 2005; 6(2): R17.  ...  Acknowledgments We thank the Lee laboratory members and Dr. Young Kwon for critical comments on the manuscript.  ... 
doi:10.12688/f1000research.12337.1 pmid:29123644 pmcid:PMC5657022 fatcat:m3phrtqvmfehbb54bqnolbo7ae
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