The Deflated Ego Problem].
How important is the concentration of RNA inside the cell? If it's a regulatory RNA then it has to bind to something and that usually means that there have to be lots of molecules.
Fei et al. (2015) looked at a model system in E. coli where a small regulatory RNA, SgrS, binds to several mRNAs and targets them for degradation.1 They looked at the binding interaction by estimating the association constant (Ka), or the dissociation constant (Kd). They also looked at the kinetics of the interaction by estimating the on-rate (kON) and the off-rate (kOFF).
Those of you who remember your introductory biochemistry class will recall that
Ka = kON/kOFF
An equilibrium is established when the on-rate and the off-rate are equal and this equilibrium is determined by the strength of the biding. If you have strong binding then more of the RNA molecules are bound and fewer are free when the equilibrium is established.
When you have a situation where a regulatory RNA has to bind to a small number of mRNAs in a cell, the binding and kinetic parameters determine the concentration of the regulatory RNA required to get significant regulation. The values of the constants they determined are quite reasonable so it serves as a good standard to judge the concentrations needed for regulation. Fei et al. concluded that in E. coli cells you need about 1000 molecules of the regulatory RNA per cell in order to regulate the mRNAs.
This number has to be larger in eukaryotic cells because the cells are bigger and there are more mRNA molecules dispersed in the cytoplasm. The results strongly suggest that most of the transcripts detected are present at too low a concentration to be effective in regulation by binding to mRNA.
There are other ways that these RNAs could be involved in regulation. For example, they could bind directly to the DNA from which they are transcribed. Or, they could bind in the nucleus, That doesn't help very much because the nucleus is also quite large relative to the targets.
Maybe the "regulatory RNAs" don't bind to anything and it's just the fact that transcription occurs at a particluar locus that causes regulation. Maybe the regulatory RNAs bind chromatin to help form three-dimensional structures in which case the strength of binding might be very high, the target numbers are small (chromosome) and only a few RNAs are needed.
There are always imaginative ways of explaining regulation by small RNAs but there is a concentration problem if they are going to bind to other RNAs or proteins. Very few of the presumptive regulatory RNAs have a high enough concentration in cells to do anything significant. They are probably junk RNA or noise.
Keep this in mind the next time you hear anyone claiming that eukaryotic geneoms are full of genes for regulatory RNAs. How, exactly, do those regulatory RNAs work if there's only a few copies per cell? We know enough about binding constants and the kinetics of binding to rule out most adaptive just-so stories.
1. Small regulatory RNAs were discovered in bacteria in the 1970s.
Fei, J., Singh, D., Zhang, Q., Park, S., Balasubramanian, D., Golding, I., Vanderpool, C. K., and Ha, T. (2015) Determination of in vivo target search kinetics of regulatory noncoding RNA. Science, 347:1371-1374. [doi: 10.1126/science.1258849]
Mattick, J.S., and Dinger, M.E. (2013) The extent of functionality in the human genome. The HUGO Journal, 7:2. [doi: 10.1186/1877-6566-7-2]
Palazzo, A. F., and Gregory, T. R. (2014) The Case for Junk DNA. PLoS Genetics, 10(5), e1004351. [doi: 10.1371/journal.pgen.1004351]