Insights provided by ribosome profiling
With these advantages and disadvantages in mind, the 
application of ribosome profiling to specific biologi-
cal questions has confirmed much of what we know 
about translation mechanism from decades of elegant 
structural, biochemical and genetic studies50.Quantitative measurement of protein synthesis rates 
over multiple time points of a dynamic process can also 
provide information about specific gene function.The 
application of this method to numerous organisms and 
cellular states has illuminated fundamental aspects of 
cell biology that were previously challenging to probe 
experimentally, providing measurements for how much 
of each protein is synthesized, how translation is regu-
lated, where synthesis starts and stops and what is being 
synthesized.Assuming that the average 
translation elongation rate is similar for different genes, 
ribosome profiling provides direct, global and quantita-
tive measurements of rates of protein synthesis, thereby 
capturing information that has been largely invisible to 
gene expression measurements of mRNA levels alone.Analysis of the 
positions of mRNAs in polysome gradients provides 
valuable complementary information to that obtained 
with ribosome profiling, but again, this method is labo-
rious and typically yields only a qualitative measure of 
protein synthesis.Other recent studies in disparate systems -- from 
the Drosophila melanogaster oocyte-to-embryo transi-
tion55 to the Trypanosome life cycle56 to the mamma-
lian cell cycle57 to plants under hypoxic conditions27
-- have used ribosome profiling to identify specific 
proteins that drive these complex processes.The latter category 
includes cellular differentiation, organismal develop-
ment and dynamic responses to cellular stress, which 
are all cases in which the instantaneous and downstream 
gene expression measurements provided by ribosome 
profiling are particularly illuminating for understanding 
molecular control.Cases in 
which ribosome profiling data provide markedly dif-
ferent information than can be obtained by traditional 
mRNA abundance measurements for gene expression 
tend to fall into two categories: systems in which tran-
scriptional regulation is minimal26,54,55; and dynamic 
cellular programmes11,12,27,35,57-59.This property of proportional synthesis, by which sub-
units of multiprotein complexes are synthesized at rates 
that are proportional to their stoichiometry in the com-
plex, turns out to be generally true for Escherichia coli
and was also observed for some (but not all) complexes 
in budding yeast (Saccharomyces cerevisiae).Subsequent 
morpholino knockdown experiments showed that 
specifically blocking translation of these three factors 
resulted in a shutdown of the first wave of zygotic tran-
scription and development, indicating that they are the 
key factors responsible for the initiation of the zygotic 
developmental programme54.As is the case for many protein complexes in 
bacteria, the eight different subunits of the Fo
F1
-ATP syn-
thase are expressed from a single polycistronic mRNA, 
and thus measurements of mRNA levels would suggest 
that the subunits are all expressed at very similar levels.For 
example, hierarchical clustering of patterns of new pro-
tein synthesis for each gene over the dynamic process of 
meiosis in budding yeast resulted in an intricate map of 
gene expression that provided highly detailed functionalHow much?3b).