Some miRNA mimics-mediated knockdown block translation instead of degrading mRNA. So you may not be able to detect changes at mRNA level if the antibody for your gene-of-interest is not available. Some reports also suggested that miRNA mimics-mediated knockdown is less potent than shRNA.

However, the miRNA mimics approach do has advantage in terms of promoter usage (Pol II instead of Poll III) and co-cistronic expression of marker or reporter gene.

Also miRNA primary transcript required both Drosha and Dicer for processing whereas shRNA only require Dicer. But this shouldn't be a problem in most of the case.

shRNAs are used primarily for knockdown. The only reason I see for using miRNAs, is to study the effect of endogenous miRNA sequences and expression.

If I recall correctly shRNAs required specific promoters (Pol III) to drive expression such as U6 or H1 where miRNA transcripts could be expressed using conventional promoters. So using miRNA derived transcripts give more flexibility in regulating expression in a certain tissue or can be adapted for inducible expression.

miRNas are more "physiological " than shRNAs as they are coded in the mammalian genome and normally expressed in cells . However miRNAs are less specific than shRNAs , they may potentially target many mRNAs at the same time , in this sense miRNAs may be more useful to target pathwaysor functions rather than single genes . Choosing one or the other depends on what one wants to achieve .

Regarding the "advantage" of expressing an shRNA vs a miRNA flanking sequences:

1. use pol II promoter, so shRNA expression can be monitored by co-expressing a marker gene such as GFP/RFP.

2. less shRNA expressed comparing with shRNA expressed by pol III promoter, may be less off-target effect.

3. sort of more "natural" since the shRNA sequence is embedded in the miRNA precursor sequence with polyA in the transcript.

Hi David

I have to echo what others have noted regarding promoter choice and regarding miR's being more 'physiological' (or rather, less artificial).

Regarding this latter point, there is evidence that whereas miRNA hairpins are efficiently exported out of the nucleus for them to enact their function, shRNAs (due to some intrinsic property, or perhaps the absense of some intrinsic property) clog up the Exportin-5 machinery. Thus with shRNA's there is a disconnect between shRNA production and action due to this artificial inefficiency within the system. Given this, it is feasible to suggest that the clogging up of the Exportin machinery may then have unintended effects on the export of other cellular miRNA's (and thus contribute to some off target effects).

Al

Structurally, shRNAs act as processed microRNAs (they are hairpins lacking the long, triling flanking regions that are removed by drosha in the pre-miRNA-miRNA step of processing), and depending on the expression construct, could be designed to be under control of a Pol II or Pol III promoter. The major physiological difference is that often miRNAs target the untranlated regions of mRNAs and do not share perfect sequence homology, resulting in a less-specific knockdown and sequestration of the target to P-bodies instead of direct degradation by RISC . Please see, for a nice review:

Methods Mol Biol. Author manuscript; available in PMC 2010 July 13.

Protein components of the microRNA pathway and human diseases

PMCID: PMC2903565

CAMSID: CAMS1325

Note this is the PubMed Canada ID number