Gene Knockdown Methods To Determine Gene Function!

A gene’s function can be defined by reducing or completely disrupting its normal expression. Since its discovery, interference RNA (RNAi) has offered a magic bullet to disrupt gene expression in many organisms. However, in recent years, new biotechnological tools have been developed for knocking down a gene thereby increasing the array of methods now available to a researcher.  

Gene knockdown methods are powerful tools that help medical scientists better understand gene function and regulation. This approach can lead to significant advancements in biology, medicine, and biotechnology.

Knocking down a gene is not merely a scientific process; it's a practical solution with real-world applications. It allows us to dissect gene function, deepen our understanding of disease mechanisms, validate therapeutic targets, and improve agricultural practices. This controlled method of studying the consequences of reduced gene expression provides invaluable insights across various research fields.

Knockdown methods, with their ability to target a gene in a cell, tissue, or organism, are versatile tools. They find extensive use in genetic research, allowing us to probe into the function of genes by observing the outcomes of their reduced expression.

Here is a list of some knockdown methods

1. RNA Interference (RNAi)

Small Interfering RNA (siRNA)

Design and Synthesis: Design siRNA sequences complementary to the selected target mRNA. The use of automated chemical synthesis ensures the production of modified and unmodified siRNA duplexes.

Transfection: This step involves introducing the siRNA into the cells using transfection protocols. These protocols, which utilize lipofection or electroporation, are used in molecular biology and genetics research for their effectiveness in gene expression regulation.

Incorporation: After transfection, the siRNA is incorporated into the RNA-induced silencing complex (RISC).

mRNA Degradation: RISC utilizes the siRNA to guide the degradation of the target mRNA, thereby significantly reducing gene expression. This method ensures productive results.

Short Hairpin RNA (shRNA)

Like RNA interference, this method involves the use of short hairpin RNA to regulate gene expression.

Vector Construction: Clone shRNA sequences into plasmid or viral vectors (like lentivirus) for vector construction.

Transduction/Transfection: Introduce the vectors into the cells. Viral vectors can integrate into the genome, providing stable and long-term knockdown.

Processing and Incorporation: The shRNA is processed into siRNA by the cellular machinery and incorporated into RISC.

mRNA Degradation: Like siRNA, the RISC complex degrades the target mRNA.

2. Morpholino Oligonucleotides

Design: Design morpholino oligonucleotides complementary to the target mRNA sequence.

Microinjection: Inject morpholinos into embryos or cells. Typically, morpholino antisense oligonucleotides are used in early developmental stages.

Translation Blockage: Morpholinos bind to the target mRNA and block its translation.

3. CRISPR Interference (CRISPRi)

Guide RNA Design: Design guide RNAs (gRNAs) that target the promoter region of the gene of interest.

dCas9-Repressor Fusion: Use a dead Cas9 (dCas9) protein fused to a transcriptional repressor domain (e.g., KRAB).

Transfection/Transduction: Introduce the gRNA and dCas9-repressor into cells via plasmid vectors or viral delivery systems.

Transcriptional Repression: The dCas9-repressor complex binds to the target DNA and inhibits transcription without cutting the DNA.

4. Antisense Oligonucleotides (ASOs)

Design: Design antisense oligonucleotides complementary to the target mRNA.

Delivery: Deliver the ASOs into cells using various transfection methods.

Binding and Inhibition: ASOs bind to the target mRNA, preventing translation or promoting degradation.

5. Transcription Factor Decoys

Design: Create synthetic oligonucleotides that mimic the binding sites of specific transcription factors.

Delivery: Introduce these decoys into cells.

Binding: The decoys bind to transcription factors, preventing them from binding to the target gene’s promoter and reducing gene expression.


Steps for Performing Gene Knockdown Experiments (A General Procedure)

Select the Target Gene: Choose the gene to be knocked down based on the research goal.

Precision is Key in the design of Knockdown Reagents. It's essential to design siRNA, shRNA, morpholinos, ASOs, or gRNAs specific to the targeted gene to ensure the accuracy of the knockdown process.

Synthesis/Cloning: Synthesize the oligonucleotides or clone the shRNA/gRNA into appropriate vectors.

Delivery into Cells: Introduce the knockdown reagents into cells using transfection (e.g., lipofection, electroporation) or transduction (e.g., lentivirus, adenovirus).

Validation is Essential: Confirmation of Knockdown. It is crucial to validate the reduction of gene expression using techniques like quantitative PCR (qPCR) for mRNA levels, Western blotting for protein levels, or functional assays to ensure the reliability of the results.

Analysis of Phenotypic Effects: To understand the gene's role, assess the biological effects of gene knockdown on cell function, viability, and phenotype.

Each method has specific protocols and optimization steps depending on the cell type, target gene, and experimental conditions. Proper controls and validation are crucial for ensuring the specificity and efficiency of gene knockdown.


Applications For Gene Knockdown Methods

Understanding Gene Function:

Functional Analysis: By reducing the expression of a specific gene, researchers can study the resulting phenotypic changes. Reducing gene expression allows researchers to determine a gene's role in various biological processes.

Gene Interaction Studies: Knockdown experiments can reveal how genes interact, providing insights into genetic pathways and networks.

Modeling Diseases:

Disease Mechanisms: Many diseases are caused by or associated with the overexpression or malfunction of specific genes. Knocking down these genes in model organisms or cell lines helps unravel the underlying mechanisms of these diseases.

Identification of Essential Genes: Cells need essential genes for survival and proliferation. Cancer cells or pathogens, in particular, need specific genes to thrive. Knocking down such genes can help identify potential therapeutic targets.

Drug Discovery and Validation:

Target Identification and Validation: Knocking down genes suspected to be involved in disease processes allows researchers to test whether these genes are viable drug targets.

Mechanism of Action Studies: Determining how drugs affect cellular processes by observing changes in phenotype after gene knockdown.

Functional Genomics:

High-Throughput Screening: Large-scale gene knockdown studies like RNAi screens help identify genes involved in specific cellular functions or disease states.

Gene Redundancy Studies: Understanding compensatory mechanisms where knocking down one gene can reveal the roles of related or redundant genes.

Developmental Biology:

Embryonic Development: Studying the effects of gene knockdown during various stages of development can reveal the roles of genes in growth, differentiation, and morphogenesis.

Tissue and Organ Development: Understanding how specific genes contribute to the formation and function of tissues and organs.

Pathway Analysis:

Dissecting Signaling Pathways: By knocking down genes involved in signaling pathways, researchers can identify the roles of individual components and how they interact within the pathway.

Agricultural Research:

Improving Crop Traits: Knocking down genes that negatively affect crop yield, disease resistance, or stress tolerance can lead to the development of better-performing plant varieties.

Pest and Disease Management: It is important to identify and manipulate genes that endow crops with resistance to pests and diseases.

Synthetic Biology:

Engineering Gene Networks: In synthetic biology, gene knockdown allows the removal or reducing the activity of endogenous genes to create space for synthetic gene circuits or to study the function of synthetic networks.

Studying Compensatory Mechanisms:

Genetic Redundancy: Knocking down a gene can help uncover how other genes compensate for its loss, providing insights into genetic robustness and redundancy.

Regenerative Medicine:

Tissue Repair and Regeneration: Knocking down genes involved in tissue repair and regeneration can help understand the genetic basis of these processes, which can aid in developing regenerative therapies.



Boettcher M, McManus MT. Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. Mol Cell. 2015 May 21;58(4):575-85. [PMC]

“This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.

Mondal, M., Peter, J., Scarbrough, O. et al. Environmental RNAi pathways in the two-spotted spider mite. BMC Genomics 22, 42 (2021).[Bmc Genomics]

“Using a sequencing-based approach, the fate of ingested RNAs was explored to identify features and conditions that affect small RNA biogenesis from external sources to better inform RNAi design.

Senapati, D., Patra, B. C., Kar, A., Chini, D. S., Ghosh, S., Patra, S., & Bhattacharya, M. (2019). Promising approaches of small interfering RNAs (siRNAs) mediated cancer gene therapy. Gene.719, 2019,144071. [Gene]

Suzuki T, Nunes MA, España MU, Namin HH, Jin P, Bensoussan N, Zhurov V, Rahman T, De Clercq R, Hilson P, Grbic V, Grbic M. RNAi-based reverse genetics in the chelicerate model Tetranychus urticae: A comparative analysis of five methods for gene silencing. PLoS One. 2017 Jul 12;12(7):e0180654.[PMC]