What is the Difference Between Gene Knockout and Knockdown

The main difference between gene knockout and knockdown is that gene knockout involves the complete erasing of target genes, or inactivating them through nonsense mutations whereas gene knockdown leads to abortive protein translation and degradation of that mRNA. Furthermore, gene knockout is applicable at DNA level while gene knockdown is applicable at RNA level.

Gene knockout and gene knockdown are two mechanisms of silencing the expression of genes inside organisms.

Key Areas Covered

1. What is Gene Knockout
     – Definition, Mechanism, Importance
2. What is Gene Knockdown
     – Definition, Mechanism, Importance
3. What are the Similarities Between Gene Knockout and Gene Knockdown
     – Outline of Common Features
4. What is the Difference Between Gene Knockout and Gene Knockdown
     – Comparison of Key Differences

Key Terms

CRISPR/Cas9, Endonucleases, Gene Knockdown, Gene Knockout, Gene Silencing, Nonsense Mutation, RNAi

What is Gene Knockout

Gene knockout is a laboratory technique of gene silencing responsible for the complete erasing of the gene from the genome or the inactivation of the gene through nonsense mutations by the introduction of frameshift mutations or stop codons to the gene sequence. As the blueprint of the gene is destroyed, the target gene product is also ablated. The method was originally developed with homologous recombination. It involves the delivery of a DNA construct, which contains the desired mutation. Then, this construct is recombined with the target gene, completely removing the gene sequence from the genome.

Figure 1: Gene Knockout

In addition, site-specific nucleases such as ZFN and TALEN can be used to knockout genes. They bind to the target DNA sequence in a highly specific manner, enhancing the efficiency of gene editing. On the other hand, the CRISPR/Cas9 system is a method of genome editing which can be used for gene knockout.

What is Gene Knockdown

Gene knockdown is another method of gene silencing responsible for the temporary inactivation of a particular gene product. It is applicable in the RNA level and it targets the mRNA produced by the transcription of the target gene. Therefore, gene knockdown is a form of post-transcriptional regulation of gene expression.

Figure 2: gene Knockdown

Significantly, it is mainly based on the RNA interference (RNAi) pathway by allowing the degradation of mRNA. Here, miRNA, siRNA, and shRNA play a key role by binding to the target mRNA. The resultant RNA duplexes are degraded by the action of Dicer and RISC. They will turn off the expression of the gene of interest temporally.

Similarities Between Gene Knockout and Gene Knockdown

• Gene knockout and gene knockdown are two mechanisms of gene silencing in cells.
• They are responsible for the regulation of gene expression at different levels.
• Therefore, they result in the alteration of the function of genes.
• Besides, both methods are used in molecular biology to alter the expression of genes of different organisms.

Difference Between Gene Knockout and Gene Knockdown

Definition

Gene knockout refers to a permanent change in DNA leading to the loss of function of a gene, caused by a manipulation of the organism’s DNA while gene knockdown refers to a temporary decrease in gene expression caused by an experimental technique, often an antisense oligo. Thus, this is the fundamental difference between gene knockout and knockdown.

Importance

The main difference between gene knockout and knockdown is that the gene knockout involves the complete erasing of the target genes or inactivating them through nonsense mutations while gene knockdown leads to abortive protein translation and degradation of that mRNA.

Effect

Furthermore, while gene knockout is a permanent method of gene silencing, gene knockdown is a temporary method of gene silencing.

Effective Level

Moreover, gene knockout is effective at DNA level while gene knockdown is effective at RNA level. Hence, this is another difference between gene knockout and knockdown.

Mechanisms

Homologous recombination, endonucleases, and CRISPR/Cas9 are several mechanisms for gene knockout while RNA interference is the main mechanism for gene knockdown. So, this is also an important difference between gene knockout and knockdown.

Conclusion

Gene knockout is a method of gene silencing applicable at the DNA level. It is responsible for the complete erasing of the target gene or inactivating them through nonsense mutations. In contrast, gene knockdown is a method of gene silencing applicable at the RNA level. It is responsible for the temporary inactivation of gene expression by degrading the mRNA. Therefore, the main difference between gene knockout and knockdown is the mechanism of gene silencing.

References:

1. Davis, E D. “Knockout by TALEN or CRISPR vs. Knockdown by ShRNA or SiRNA.” Genecopoeia, GeneCopoeia, Inc., 2014, Available Here.

Image Courtesy:

1. “Frameshift mutations (13080927393)” By Genomics Education Programme – Frameshift mutations (CC BY 2.0) via Commons Wikimedia  
2. “Mechanism of RNA interference” By Simone Mocellin and Maurizio Provenzano – RNA interference: learning gene knock-down from cell physiology doi:10.1186/1479-5876-2-39 (CC BY 2.0) via Commons Wikimedia