Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
The RNA interference (RNAi) pathway in animal cells can be harnessed to silence gene expression with artificial small interfering RNAs (siRNAs) or transgenes that express small hairpin RNAs (shRNAs). The transgene-expressing shRNA approach has been adapted into large-scale resources for genome-wide loss-of-function screens, whereas focused studies on a narrow set of genes can be achieved by using individual shRNA constructs from these resources. Although current shRNA repositories generally work, they might fail in certain situations and therefore necessitate other alternatives. We detail here a new highly-accessible and rational design of custom shRNAs that utilizes a refined backbone configuration termed the 'organic' shRNA (OshR) platform. The OshR platform is 'organic' because it conforms more naturally to the endogenous vertebrate miRNAs by maintaining specific bulges and incorporating strategic mismatches to insure the desired guide strand is produced while reducing the accumulation of passenger strands that might contribute to off-target effects. We also demonstrate that the reliability of the OshR platform for gene silencing is increased when sequences target the 3' UnTranslated Region (3'UTR) of a gene. We further compare the OshR platform with the current and emerging shRNA designs, and propose that the OshR platform is a novel approach that can allow investigators to generate custom and effective shRNAs for individual gene functional studies.
Adamson,
A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response.
2012, Pubmed
Adamson,
A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response.
2012,
Pubmed Bartel,
MicroRNAs: target recognition and regulatory functions.
2009,
Pubmed Bartel,
MicroRNAs: genomics, biogenesis, mechanism, and function.
2004,
Pubmed Bergauer,
Analysis of putative miRNA binding sites and mRNA 3' ends as targets for siRNA-mediated gene knockdown.
2009,
Pubmed Bernards,
shRNA libraries and their use in cancer genetics.
2006,
Pubmed Brummelkamp,
A system for stable expression of short interfering RNAs in mammalian cells.
2002,
Pubmed Cai,
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs.
2004,
Pubmed Carthew,
Origins and Mechanisms of miRNAs and siRNAs.
2009,
Pubmed Chang,
Lessons from Nature: microRNA-based shRNA libraries.
2006,
Pubmed Cheloufi,
A dicer-independent miRNA biogenesis pathway that requires Ago catalysis.
2010,
Pubmed Chiang,
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.
2010,
Pubmed Cifuentes,
A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.
2010,
Pubmed Cleary,
Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.
2004,
Pubmed Dickins,
Tissue-specific and reversible RNA interference in transgenic mice.
2007,
Pubmed Dietzl,
A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.
2007,
Pubmed Elbashir,
RNA interference is mediated by 21- and 22-nucleotide RNAs.
2001,
Pubmed Elbashir,
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells.
2001,
Pubmed Faunes,
Characterization of small RNAs in Xenopus tropicalis gastrulae.
2012,
Pubmed
,
Xenbase Fellmann,
Functional identification of optimized RNAi triggers using a massively parallel sensor assay.
2011,
Pubmed Fish,
Short-term cytotoxic effects and long-term instability of RNAi delivered using lentiviral vectors.
2004,
Pubmed Förstemann,
Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein.
2005,
Pubmed Garcia,
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.
2011,
Pubmed Ghildiyal,
Small silencing RNAs: an expanding universe.
2009,
Pubmed Grimm,
Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways.
2006,
Pubmed Grimson,
MicroRNA targeting specificity in mammals: determinants beyond seed pairing.
2007,
Pubmed Gu,
Thermodynamic stability of small hairpin RNAs highly influences the loading process of different mammalian Argonautes.
2011,
Pubmed Gu,
The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo.
2012,
Pubmed Gu,
Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs.
2009,
Pubmed Harborth,
Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.
2003,
Pubmed Helwak,
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.
2013,
Pubmed Hu,
A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal.
2009,
Pubmed Kedde,
RNA-binding protein Dnd1 inhibits microRNA access to target mRNA.
2007,
Pubmed Kertesz,
The role of site accessibility in microRNA target recognition.
2007,
Pubmed Khvorova,
Functional siRNAs and miRNAs exhibit strand bias.
2003,
Pubmed Kim,
Biogenesis of small RNAs in animals.
2009,
Pubmed King,
Tyrosinase gene mutations in oculocutaneous albinism 1 (OCA1): definition of the phenotype.
2003,
Pubmed Lau,
Small RNAs in the animal gonad: guarding genomes and guiding development.
2010,
Pubmed
,
Xenbase Lee,
MicroRNA genes are transcribed by RNA polymerase II.
2004,
Pubmed Leung,
Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs.
2011,
Pubmed Li,
Defining the optimal parameters for hairpin-based knockdown constructs.
2007,
Pubmed Lund,
Limiting Ago protein restricts RNAi and microRNA biogenesis during early development in Xenopus laevis.
2011,
Pubmed
,
Xenbase McBride,
Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: implications for the therapeutic development of RNAi.
2008,
Pubmed Moffat,
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.
2006,
Pubmed Neumüller,
Genome-wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi.
2011,
Pubmed Ni,
A genome-scale shRNA resource for transgenic RNAi in Drosophila.
2011,
Pubmed Nielsen,
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs.
2007,
Pubmed Obernosterer,
Target site effects in the RNA interference and microRNA pathways.
2008,
Pubmed Oetting,
The tyrosinase gene and oculocutaneous albinism type 1 (OCA1): A model for understanding the molecular biology of melanin formation.
2000,
Pubmed Okamura,
The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution.
2008,
Pubmed Okamura,
Distinct mechanisms for microRNA strand selection by Drosophila Argonautes.
2009,
Pubmed Paddison,
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells.
2002,
Pubmed Paddison,
siRNAs and shRNAs: skeleton keys to the human genome.
2003,
Pubmed Paddison,
Stable suppression of gene expression by RNAi in mammalian cells.
2002,
Pubmed Paddison,
A resource for large-scale RNA-interference-based screens in mammals.
2004,
Pubmed Perrimon,
In vivo RNAi: today and tomorrow.
2010,
Pubmed Premsrirut,
A rapid and scalable system for studying gene function in mice using conditional RNA interference.
2011,
Pubmed Robins,
Incorporating structure to predict microRNA targets.
2005,
Pubmed Root,
Genome-scale loss-of-function screening with a lentiviral RNAi library.
2006,
Pubmed Schwarz,
Asymmetry in the assembly of the RNAi enzyme complex.
2003,
Pubmed Silva,
Second-generation shRNA libraries covering the mouse and human genomes.
2005,
Pubmed Siolas,
Synthetic shRNAs as potent RNAi triggers.
2005,
Pubmed Solimini,
Recurrent hemizygous deletions in cancers may optimize proliferative potential.
2012,
Pubmed Stegmeier,
A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells.
2005,
Pubmed Tafer,
The impact of target site accessibility on the design of effective siRNAs.
2008,
Pubmed Tan,
Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy.
2012,
Pubmed Tyler,
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci.
2008,
Pubmed Xia,
Calcium influx via the NMDA receptor induces immediate early gene transcription by a MAP kinase/ERK-dependent mechanism.
1996,
Pubmed Yang,
Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates.
2010,
Pubmed Yang,
Functional parameters of Dicer-independent microRNA biogenesis.
2012,
Pubmed Yang,
Widespread regulatory activity of vertebrate microRNA* species.
2011,
Pubmed Yang,
Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants.
2011,
Pubmed Yang,
Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis.
2010,
Pubmed
