Nuclear export is a limiting factor in eukaryotic mRNA metabolism
Fig 2
Nuclear RNA half-lives are longer than cytosolic half-lives.
(A) Nuclear and cytosolic RNA half-life estimates of 3’UTRs. Half-lives were averaged over both measured time series. Gray dots represent unreliable estimates, yellow dots correspond reliable estimates for nuclear half-life, and green dots portray reliable estimates for both nuclear and cytosolic compartment (see Methods for reliability criteria). The half-life estimate distributions are given at the top and right hand side, color representation as in scatterplot. The solid and dashed lines indicate median half-life estimates of reliable and all 3’UTRs, respectively. (B) Nuclear by cytosolic half-life ratios of all 3’UTRs (gray) and 3’UTRs with reliable half-life estimates (green) for both compartments. The solid and dashed lines indicate median half-life ratios of reliable and all 3’UTRs, respectively. (C) Comparison between half-life estimates by our two-compartment model and whole-cell extract half-life measurements from Schueler et al. (2014) [38]. Our nuclear and cytosolic RNA estimates were summed to generate pseudo-whole-cell estimates. Gray dots represent unreliable estimates, green points represent reliable estimates. (D) Correlation of half-lives between 3’UTRs and exonic or intronic peaks of the same gene. Only 3’UTRs and peaks that had one unique gene annotation were considered. Data points are colored by whether the 3’UTR harbors one (gray) or multiple (blue) expressed 3’UTR peaks. (E) Estimation of the RNA ratio using a spherical median. Each dot represents the angular coordinates of a 3d unit vector, which in turn is determined as the normal vector of a plane spanned by three triplets
of three randomly sampled 3’UTRs gi, i = 1, 2, 3. Contour lines show locations of constant
RNA ratio. The red dot is the spherical median of the sampled normal vectors and corresponds to a ratio of 0.66. Azimuth angles ψ ∈ [π, 2π] correspond to normal vectors v in which not all entries are positive and are omitted. (F) Fraction of non-negative nuclear degradation rate estimates as a function of the
RNA ratio. Assuming at least 50% positive estimates (orange horizontal line) leads to a maximum admissible ratio of 0.2 (orange vertical line).