7.3 RNAi and other gene silencing techniques

RNA interference (RNAi) is a powerful gene silencing technique that revolutionized functional genomics. It uses small RNA molecules to target and degrade specific mRNAs, allowing researchers to study gene function by knocking down expression.

RNAi has several advantages for genetic screens, including ease of use, specificity, and applicability across many organisms. However, it also has limitations like off-target effects and incomplete silencing. Understanding RNAi's principles and applications is crucial for modern genomics research.

RNA interference: Principles and Mechanisms

RNAi Pathway and Key Components

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• RNAi is a biological process in which RNA molecules inhibit gene expression or translation by neutralizing targeted mRNA molecules through complementary base pairing
• The RNAi pathway is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short interfering RNAs (siRNAs) or microRNAs (miRNAs)
• siRNAs and miRNAs are incorporated into the RNA-induced silencing complex (RISC), where they guide the cleavage or translational repression of complementary mRNA targets
  • siRNAs typically have perfect complementarity to their mRNA targets, leading to mRNA cleavage and degradation (e.g., siRNA targeting a specific viral gene)
  • miRNAs often have imperfect complementarity to their targets, resulting in translational repression or mRNA destabilization (e.g., miRNA-122 regulating cholesterol metabolism)

Conservation and Biological Roles of RNAi

• RNAi is a highly conserved mechanism across many eukaryotic organisms, serving as a natural defense against viral infections and playing a role in gene regulation
• In plants, RNAi acts as an antiviral defense mechanism by targeting and degrading viral RNA (e.g., RNAi against Tobacco Mosaic Virus)
• RNAi also plays a crucial role in regulating endogenous gene expression during development and in response to environmental cues (e.g., miRNA-mediated regulation of flowering time in plants)
• The discovery of RNAi has revolutionized our understanding of gene regulation and has led to the development of powerful tools for studying gene function and potential therapeutic applications

RNAi Approaches: siRNA vs shRNA vs miRNA

siRNA and shRNA

• siRNAs are short, double-stranded RNA molecules (usually 21-23 nucleotides) that are directly introduced into cells to induce RNAi
  • They are often chemically synthesized and have a transient effect on gene silencing (e.g., siRNA targeting GAPDH for transient knockdown)
• shRNAs are short hairpin RNA molecules expressed from DNA vectors
  • They are processed by Dicer into siRNAs and can achieve stable, long-term gene silencing through continuous expression (e.g., shRNA targeting p53 for stable knockdown)
• Both siRNAs and shRNAs rely on the RNAi machinery for gene silencing and are typically designed to target a specific gene

miRNA

• miRNAs are endogenous, single-stranded RNA molecules (usually 22 nucleotides) that regulate gene expression post-transcriptionally
  • They are processed from longer primary miRNA transcripts (pri-miRNAs) and can target multiple mRNAs (e.g., miRNA-34 family regulating cell cycle and apoptosis)
• miRNAs are part of the endogenous gene regulatory network and can regulate multiple genes simultaneously due to their imperfect complementarity
• The seed region (nucleotides 2-8) of miRNAs is critical for target recognition and binding (e.g., seed region of let-7 miRNA family is highly conserved across species)

RNAi for Gene Knockdown and Phenotype Analysis

Designing and Delivering RNAi Reagents

• Designing effective siRNAs or shRNAs requires consideration of factors such as target sequence specificity, thermodynamic stability, and potential off-target effects
  • Algorithms and design tools (e.g., siDESIGN, shRNA Designer) can help optimize RNAi reagent design
• Delivery methods for RNAi reagents include lipid-based transfection, electroporation, and viral vectors (e.g., lentiviruses or adenoviruses) for stable expression of shRNAs
  • Lipid-based transfection reagents (e.g., Lipofectamine) facilitate siRNA delivery into cells
  • Viral vectors (e.g., lentiviral shRNA) enable stable and long-term gene silencing

RNAi Screens and Phenotypic Analysis

• High-throughput RNAi screens using siRNA or shRNA libraries can be employed to identify genes involved in specific biological processes or diseases
  • Genome-wide RNAi screens have been used to identify essential genes in cancer cell lines (e.g., Project Achilles)
• Phenotypic analysis after RNAi-mediated gene silencing can involve various assays, such as cell viability, proliferation, migration, or specific functional readouts relevant to the gene of interest
  • Cell viability assays (e.g., MTT, CellTiter-Glo) can assess the effect of gene knockdown on cell survival
  • Migration assays (e.g., wound healing, transwell) can evaluate the role of genes in cell motility
• Rescue experiments, in which an RNAi-resistant version of the target gene is introduced, can help validate the specificity of the observed phenotype
  • Synonymous mutations in the RNAi target site can render the gene resistant to RNAi-mediated silencing

RNAi Advantages and Limitations

Advantages of RNAi

• RNAi offers a rapid, cost-effective, and scalable approach for gene silencing compared to traditional gene knockout methods like homologous recombination
  • RNAi reagents can be easily designed and synthesized, enabling quick interrogation of gene function
• RNAi can be used to target virtually any gene of interest, including those that are essential for cell survival or development, which may be challenging to study with knockout approaches
  • Essential genes (e.g., DNA replication factors) can be studied using inducible or partial RNAi-mediated knockdown
• RNAi allows for the study of gene function in a wide range of organisms, including those for which genetic manipulation tools are limited
  • RNAi has been successfully applied in diverse organisms (e.g., C. elegans, Drosophila, plants, mammals)

Limitations and Alternative Approaches

• Off-target effects, where unintended genes are silenced due to sequence similarity, can be a limitation of RNAi and require careful design and validation of RNAi reagents
  • Multiple independent RNAi reagents targeting the same gene can help mitigate off-target effects
• The efficiency of gene silencing by RNAi can vary depending on the target gene, cell type, and delivery method, and complete knockdown is not always achievable
  • Optimization of RNAi reagent design and delivery can improve silencing efficiency
• Alternative gene silencing methods, such as CRISPR-Cas9-mediated gene editing, can offer more precise and complete gene inactivation but may require more time and resources to implement
  • CRISPR-Cas9 can introduce targeted mutations or deletions for permanent gene knockout (e.g., CRISPR knockout of essential genes in cancer cells)
  • CRISPR interference (CRISPRi) can achieve gene silencing by targeting catalytically inactive Cas9 to the gene promoter or coding region