There is no clear difference as far as I can see. To me a knockout is the complete deletion of a gene (all exons all introns). A gene silencing can be the deletion of a functional (or assumed functional) part of the gene like to delete the PAS domain in eg. the period 1 gene (the PAS domain is thought to carry all or most of the function of this gene). Another use for the term "gene silencing" is the reduction of gene activity by siRNA or shRNA, where the gene is not completely inactivated but strongly reduced. Some say silencing begins at 70% reduction of the amount of mRNA. There are probably other definitions.

Dear Saurav,

Its very simple gene silenecing is the natural process where the ability of a cell to prevent the expression of a certain gene Gene silencing can occur during either transcription or translation WHEREAS gene knockout is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism).

So one occurs naturally and other occurs forcefully( manipulation)..

Regards,

Sanketh D.S

Dear Erik,

Thank you so much. I am doing work of expression of clock genes of fish,so if I want to observe that after silencing of the clock genes of the particular fish tissue. So what is the best method between silencing and knockdown for the observation of the gene expression of certain clock genes? Knockdown means I want to remove those genes from the particular tissue.

Regards,

Dear Sanketh,

Thanks

Dear Saurav,

you are right, the genes have to be knocked out for your purpose. In fish there may be other techniques useful like morpholino stuff. Also CRiSpR/CAS may be useful, but I am no expert on that. Best wishes, Erik

While I principally agree with Eric above, adding to the topic I would suggest the way I would understand this, is that usually the term "Repression" is used when we are talking about short-term (promoter-driven?) regulation, which is usually over after cells have divided. While "Silencing" would refer to a more permanent gene inactivation (enhancer-driven?), which lasts for many cell divisions and becomes part of the cells identity. That would usually be mediated by epigenetic mechanisms, such as heterochromatinization of those genes (via PRC2 and PRC1and H3K9/H3H27me3/HP1a) which are not used even damaging in the specific lineage the cell has become.

But careful, I am not sure if there is a general consensus about this view. Personally when deleting a gene I would use neither, as absent genes are simply absent so it makes no sense for me to say they are "silenced" or "repressed" (Both referring to a gene which is THERE in the first place)

Hope, I did not add to the confusion.

All the best, Thomas :-)

As most of people write above, "Silencing" would refer to an epigenetic lock of a gene (through histone/DNA modifications). This can be the case of a "neural gene" (e.g. Ngn1, GFAP) "silenced" in a progenito muscle cell, since such "neural gene" is unuseful for the activit of a muscle cell precursor/myofibre. In contrast, gene knockout is the result of a biotechnological modificatio done by scientists (e.g. using CRISPR etc...). Good luck