Microarrays And Gene Regulation

Question

[Ketil]

Recently, it occured to me that one reason microarrays often only show vague changes in gene expression is that gene regulation is often done by miRNA silencing of genes, rather than changes in level of expressed mRNA. I believe microarrays typically measure known mRNAs, and unless the array also contains relevant miRNAs, you're missing a lot of possibly crucial information.

Is this correct?

If so, do microarrays these days usually come with miRNA probes? How complete is our knowledge of miRNAs, anyway? And given today's densities, why not just include reverse-complement probes for the 3' UTR (where miRNAs usually bind)?

Answer 1

[Chris Evelo]

Just to add to the answers already given:

• One of the silencing mechanisms for miRNA's can result in breakdown of mRNA, which will of course affect the amount of mRNA measured (the mRNA measurement in that case detects the net effect of transcription and miRNA regulation).
• I recently heard a brilliant talk by Mats Lundman (opening talk at SBMCTA in Sao Pedro, Brazil) who showed a mechanism where miRNA are transcribed downstream of the mRNA they are targeted against, thereby leading to a kind of burst time in mRNA availability. So I don't fully agree with @lyco's remark that different regulations mostly are in the same direction. Fine tuning may actually be opposite and time regulated.

Answer 2

[Lyco]

No, I don't think that this is correct. (Disclosure: I do microarrays for a living so you might consider me biased). Without any doubt is there posttranscriptional regulations by miRNAs, but in most cases this contribution is minor. There are other posttranslational factors that govern protein levels, which are independent from the mRNA amount and thus cannot be measured by transcriptomics approaches (most important: protein half life, but also various sources of translational regulation.

• Thus, if you are interested in protein levels, microarrays are not the way to go.
• If you are interested in 'protein level changes', microarrays are not optimal but can give a reasonable approximation. Note: if there is a biologically meaningful induction of a gene's mRNA, this is rarely counteracted by posttranscriptional factors - often transcriptional and translational controls point in the same direction.
• Finally, there are a number of questions where microarray are very good: responses to drugs and toxins (often regulated on the mrNA level), assessment and specificity of epigenetic silencing, mRNA stability (n.b: microarrays measure steady state mRNA levels, not transcriptional rate) and general 'transcriptional responses' (to inflammation, DNA damage, senescences, ...)

Compare this related blog post

Answer 3

[Neilfws]

1. I would not say that microarrays "often only show vague changes in gene expression." Depending on how the experiment is designed, very significant fold-changes can be observed. What is true is that often, only a relatively small fraction of probes show differential expression, but that's exactly what you'd expect if a subset of genes in particular pathways are responding to changed conditions.
2. Microarrays do not "come with" miRNA probes, but there are custom arrays and vendor platforms designed to detect miRNA. Here's an article that compares 6 such platforms.
3. Our knowledge of miRNAs is very incomplete. Many have been predicted from sequence analysis, but very few validated or assigned biological functions. There's a rather overwhelming literature on this topic, but I'd start with some miRNA databases such as microRNA.org.
4. I think 3'-UTR binding would give a very noisy signal on microarrays, but see point (2), there are miRNA array platforms.

[Ketil]

Heh, regarding #1, I didn't intend to be provocative. I'm not very familiar with microarray analysis, but I've attended a few talks trying to wring information out of experiments - at least in those cases, the results seemed inconclusive and not easily reproducible. This could of course be due to complex interactions (as opposed to simple, single-gene explanations).

[David Quigley]

@neilfws: Actually, some microarrays do come with miRNA probes, although it's not clear to me how useful they are. See Measuring Microrna Expression On Affymetrix Gene St Chips

Answer 4

[Paul]

Actually 84% of miRNA silencing is by mRNA degradation, which would be picked up by microarrays. See this paper: http://www.nature.com/nature/journal/v466/n7308/full/nature09267.html