Three terms are getting a mixed up in this discussion. 1. Knockdown - reduction in expression without modifying DNA of the locus itself, by morpholino or siRNA for example. 2. Deletion - loss of a chunk of DNA. that "chunk" can contain part of a gene, whole gene or several genes, and an be achieved through genetic engineering or randomly. 3. Knockout - a fancy term mouse geneticists chose to use to describe inactivation of a gene at the DNA level, usually by deleting an exon.

In yeast genetics, the classical term is "gene disruption". It describes inactivation of a gene through homologous recombination- which is kind of the same thing as mouse knockout.

CRISPRs, TALENs and the like are most often used to induce small deletions. Term "knockdown" is definitely not applicable to them, but I do not think there is a consensus as to what term to use- other than "mutant" of course.

In simple terms, deletion strains don't have the gene itself (removal/disruption).This can be done either by  homologous recombination to remove gene or gene disruption by mutation/INDEL.

While in knockout strains gene is present but we silence the effect of gene either at transcription level ( by changing promoter)  or at mRNA level (siRNA/miRNA, etc.) or at protein level( using specific protease genes etc.).

Various other methods are there, but these are most common one's.

Thanks Shyam, I thought in the knockout strain the whole gene it self is removed or replaced and in the deletion strain, part of the gene is removed.  But I'm still a bit confused with this terminology. There are numbers of articles use these terms differently.

I agree with Shyam's answer except when referring to RNA and protein level. The reduction of RNA/protein without effecting DNA is more often called knockdown (using techniques like RNAi, CRISPR, TALEN). Knockout is the term used for alterations made at the DNA level which render a gene inactive.

Thanks Pawel

Since you you talk of strains, I guess you refer to yeast or E. Coli. In Drosophila or Mouse genetics we don't use the terminology deletion strain, so probably a yeast expert will explain it to you best..

Anyway in genetic terms the deletion strain is a strain engineered to carry a deletion in a gene. The deletion is in the majority of the cases engineered in order to obtain the knockout of gene expression... In other words if in consequence of the deletion you don't obtain the product of your gene (the protein), you actually have a knockout strain, and the two terms coincide.

Anyway, in principle a genetic deletion will not necessary generate a knockout, it depends on how you design it, you might want to delete a specific domain in a gene and obtain an hypomorph, a dominant negative, a gain of function...

Hi Dilshan

Your doubt is very understandable. I believe what you want to know is if by crossing mice you obtain a mutation that will be transmitted to the next generation. To achieve that you must use CMV-Cre mice, often called Cre-deleter, because the mutation will be transmitted. It goes germ-line while other Cre strains are specific to certain genes / organs or structures, hence it will not be transmitted.

Does this answer your question?

I think mixing Crispr-Cas9 and other techniques is a different story but I can get into it if necessary.

Cheers, Alex

Three terms are getting a mixed up in this discussion. 1. Knockdown - reduction in expression without modifying DNA of the locus itself, by morpholino or siRNA for example. 2. Deletion - loss of a chunk of DNA. that "chunk" can contain part of a gene, whole gene or several genes, and an be achieved through genetic engineering or randomly. 3. Knockout - a fancy term mouse geneticists chose to use to describe inactivation of a gene at the DNA level, usually by deleting an exon.

In yeast genetics, the classical term is "gene disruption". It describes inactivation of a gene through homologous recombination- which is kind of the same thing as mouse knockout.

CRISPRs, TALENs and the like are most often used to induce small deletions. Term "knockdown" is definitely not applicable to them, but I do not think there is a consensus as to what term to use- other than "mutant" of course.

Thanks for the comments, it was very informative

Hi there,

I think the difference between the two is very subtle and is related to gene structure . The deletion strain  imposes that the gene targeted has lost a portion of its coding sequence leading to the loss of function because that's what deletion means. The knockout strain definition is more vague as it just indicates that the gene isn't functional anymore whatever the technique used to obtain this strain (deletion, disruption, promoter inactivation). To sum up I would say that deletion can be used to generate a knockout whereas you can generate a knockout without considering any deletion.

Deletion in E.coli, is removal of the gene and you cann't find that sequence in subsequent DNA replication step.

Knockout: Inactivating and making it inoperable. Usually it confirmed by addition of particular gene marker like Kanamycin, ampicillin amoxicillin, tetracycline and or any toxic agent sensitivity or resistance.