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Forum - siRNA, microRNA and RNAi

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Explore Open Questions @ NYAS

• Design & Pitfalls

  • How good are the algorithms for predicting miRNA binding targets?

  • Alternative approach to generate shRNA from cDNA

  • Retroviral delivery of small interfering RNA into primary cells

  • RNAi cytotoxicity & instability using lentiviral vectors

  • Rational siRNA design for RNAi

  • Alleviating interferon response & maintaining efficacious siRNA response

  • Delivery & Specificity

• Large Scale/High Content/High-Throughput Screens (HTS)

  • Genome-wide RNAi Global Initiative

  • Genome-wide RNA-interference Based Screen for Genes Important in Cell Division (EMBL)

  • Genomewide Profiling After Gene Knockdown by RNAi
  • RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells
  • MicroRNA expression microarray for mammalian brain
  • RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells
  • siRNA cell arrays for high-content screening microscopy
  • Using microarrays to screen for RNAi
  • Parallel Chemical Genetic and Genome-Wide RNAi Screens Identify Cytokinesis Inhibitors and Targets
  • Functional Dissection of an Innate Immune Response
  • Genome-wide RNAi analysis of C. elegans fat regulatory genes
  • A large-scale RNAi screen in human cells identifies new components of the p53 pathway
  • Resource for large-scale RNA-interference-based screens in mammals
  • Growth & Viability - Genome-Wide
  • Hedgehog signaling - Genome-scale

• Post-Transcriptional Pathway/Player updates

  • Signaling - Signaling Update and Data Center at Nature

  • Loquacious, a Double-Stranded RNA-Binding Domain Protein required for Normal microRNA Maturation and Germ-Line Stem Cell Maintenance

  • Dicer-1–Loquacious Complex Process Pre-microRNAs

  • MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies

  • mRNA Turnover Meets RNA Interference

  • Argonaute and Its Implications for RISC Slicer Activity

  • Argonaute Journeys into the Heart of RISC

  • Argonaute2 Is the Catalytic Engine of RNAi

  • Plant miRNA surprises

  • Overhang-specific small interfering RNA recognition by the PAZ domain

  • RISC: a 5' phosphomonoester-producing RNA endonuclease

  • RNAi takes Evo-Devo World by Storm

  • Human genes hit the big screen

  • Armitage is required for RISC

  • RNase negatively regulates RNAi

  • Sequence-Specific Inhibition of Small RNA Function

• Transcriptional Pathway/Player updates

  • Signaling - Signaling Update and Data Center at Nature

  • The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

  • A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline

  • Characterization of the piRNA Complex from Rat Testes

  • Methylation mystery: miRNA vs. siRNA - see model

  • RITS acts in cis to promote RNAi-mediated transcriptional and post-transcriptional silencing

  • Induction of DNA methylation and gene silencing by short interfering RNAs in human cells

  • Emergence of alternate pathways

  • SiRNA silencing in human cells

  • Transcriptional Activation by Small dsRNA

  • Repression by non coding RNA

  • Chromatin packaging depends on RNAi

  • Heterochromatin Targeting

  • Transposable elements in heterochromatin and epigenetic control

• Pathways/Players for transcriptional & posttranscriptional RNAi

  • Micro RNAs may have a crucial role in the signaling processes that govern vertebrate cell fate decisions

  • A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in S. pombe

  • Wnt Signaling Glows with RNAi

• RNAi Therapeutic Models

  • Reviews listed at PubMed
  • Therapeutic potential of siRNA-mediated transcriptional gene silencing
  • RNA interference: a potential therapeutic tool for silencing splice isoforms linked to human diseases
  • RNAi as a treatment for HIV-1 infection
  • Therapeutic potential of RNAi in metabolic diseases
  • Toward silencing the burden of malaria: progress and prospects for RNAi-based approaches

  • RNAi Therapeutics

  • Can companies deliver on the RNAi business?

  • RNAi In Vivo Applications

  • RNAi as a gene therapy approach

  • eiRNAi

  • RNAi turns poppies off morphine

  • A cholesterol connection in RNAi - Therapeutic Silencing of endogenous gene

  • Silencing Cancer - multidrug-resistant

  • Novel RNAi Therapy: Intron-Derived MicroRNA Drugs

  • Tailor-made Riboswitches

• C. elegans - Fabio Piano's Database

  • Phenotype Search

  • PhenomicDB

  • Signaling - Signaling Update and Data Center at Nature

• Cell division related genes - Hyman RNAi

• Codex - Curates publicly available RNAi resources 

• Drosophila

  • GenomeRNAi Database 2006

  • microRNA targets

  • RNAi finder

  • RNAi Collection - Over 7,200 Drosophila dsDNA constructs

  • Signaling - Signaling Update and Data Center at Nature

• miRNA

  • Registry

  • Cell fate decisions

  • Cloned from mouse and human

  • Drosophila microRNA targets

  • Human microRNA targets

  • siRNA target sequences (human, mouse, rat)

  • Signaling - Signaling Update and Data Center at Nature

• Phenomic database - model organisms

• Plant Chromatin DB - RNAi Lines & Vectors

• Reactome: bio-processes knowledgebase

• RNA World

• shRNA (Short Hairpin RNA)

  • Alternative approach to generate shRNA from cDNA

  • Codex - Curates publicly available RNAi resources

  • Human and Mouse Libraries

  - also see NCI site

  • Signaling - Signaling Update and Data Center at Nature

• siRNA

  • Database - McManus Lab

  • Database - Trono lab

  • siRNA Sequence Finder (Jack Lin's)

  • User guide - Tuschl lab

• Signaling - Signaling Update and Data Center at Nature

Other databases

Human and Mouse Short Hairpin RNA Libraries

Human microRNA targets

Nucleofector™ technology (Amaxa)

Sequence Finder (Jack Lin's)

RNAi Station - articles, Protocols, Bioinformatics

Small Interference RNA Resources Portal from Ion Channel Group

Systems; Mechanisms; Studies; Protocols

Synthesis