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I know that researchers learn gene regulatory networks from microarray experiments that measure the mRNA expression levels. However, I do not understand how mRNAs regulate each other's levels. Do they affect the transcription step or the translation step? I know that there are transcription factors which affect the transcription step, but those are not mRNAs but proteins. How does an mRNA (the product before translation) affect another mRNA's expression level? Is this regulation process very similar to the regulation by microRNAs?

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  • $\begingroup$ You say that "researchers learn gene regulatory networks from microarray experiments". I do not believe this is true. Microarray experiments just indicate which mRNAs increase or decrease in expression in a given situation. I suggest you either cite a paper to support your contention, delete the first sentence of your question or change the question to "How do microarray experiments show..." (to which I would say the answer is that they don't). $\endgroup$
    – David
    Oct 3, 2016 at 21:02
  • $\begingroup$ @David: We can argue about whether folks actually learn gene regulatory networks from these experiments, but they definitely claim to! $\endgroup$ Oct 4, 2016 at 13:09
  • $\begingroup$ Yes, they claim to, that is what I mean. Bu the first sentence is not really the point here. We can even completely delete that sentence if that is confusing. What I am wondering is whether mRNAs have any regulatory role on gene transcription before they are translated to proteins. $\endgroup$
    – user5054
    Oct 4, 2016 at 22:54

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Typically, these experimenters aren't thinking that the mRNAs directly regulate each others' expression levels, but rather that the proteins they code for affect expression. They're just mRNA as a proxy for the corresponding protein.

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  • $\begingroup$ Thanks! Don't the mRNAs regulate gene expression at all while they are mRNAs (before being translated to proteins)? Maybe there are mRNAs transcribed but that are not translated at all, and have some function in gene regulation? Do you have any ideas? $\endgroup$
    – user5054
    Oct 3, 2016 at 3:30
  • $\begingroup$ I am a beginner and I liked your question. As @Daniel Weissman pointed out, proteins are coded by mRNAs, so the proxy is such a powerful analogy here. A coding error (horror), as it seems. $\endgroup$
    – bonCodigo
    Oct 3, 2016 at 6:23

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