Figure 6. Classification of nuclear targets by relative similarity to early or late nuclear intermediates.

(A) Venn diagram showing the number of significant targets detected in 2DTM searches with the indicated templates. Overlap indicates targets identified in two or more searches. (B) Venn diagrams showing the number of significant targets detected in 2DTM searches with the indicated templates in the nucleus (left) and cytoplasm (right). (C) Scatterplot showing the log₂(EN 60S / LN 60S 2DTM SNR) values relative to the log₂(mature 60S / LN 60S 2DTM SNR) values for each EN, LN and mature 60S-detected target. Ellipses indicate the fits of three Gaussians and each concentric ellipse indicates one standard deviation from the mean. Each target is colored according to its most likely class membership. (D) Heat map showing the probability of each of the targets examined in (C) belonging to one of the populations, EN, LN or mature 60S. Targets are grouped by their subcellular localization, followed by their classification as EN 60S (purple), LN 60S (light blue), or mature 60S (yellow). (E) Cryo-EM micrograph of the yeast nuclear periphery from a FIB-milled lamella shown in in Figure 1, displaying the results of 2DTM searches, colored by their classification as mature 60S (yellow), LN 60S (blue) or EN 60S (purple) based on their relative 2DTM SNRs. (F) Boxplot showing the nuclear density of EN 60S (purple), LN 60S (light blue), and mature 60S (yellow) detected targets before classification in the indicated cells. (G) Bar chart showing the proportion of the LN 60S-detected targets in the indicated cells that are classified as LN 60S (blue), mature 60S (yellow), or EN 60S (purple).

Figure 6—figure supplement 1. Relative similarity to EN, LN and mature 60S distinguishes the nuclear and cytoplasmic 60S populations.

(A) TEM image of the nuclear periphery shown in Figure 1, overlaid with EN 60S detected targets in purple. (B) Violin plots showing the kernelled distribution of 2DTM SNRs for EN 60S-detected targets in the indicated subcellular compartment. ****: p<0.0001. (C) Histogram showing the distribution of log₂(EN 60S / LN 60S SNR) values of EN and LN 60S-detected targets in untreated cells. Targets are grouped by their subcellular distribution. (D) As in (C), showing the distribution of log₂(mature 60S / EN 60S SNR) values of mature 60S and EN 60S detected targets. (E) Bar chart showing the proportion of cytoplasmic 60S-detected targets in the indicated cells that are classified as LN 60S (blue), mature 60S (yellow), or EN 60S (purple).

Figure 6—figure supplement 2. Additional image showing results of classification using EN, LN and mature 60S.

(A) TEM image of the nuclear periphery. Scale bar indicates 50 nm. (B) The image in (A) is shown overlaid with EN 60S-detected targets in purple, (C) LN 60S-detected targets in blue or (D) mature 60S-detected targets in yellow. (E) As in (B) showing the results of 2DTM searches, colored by their classification as mature 60S (yellow), LN 60S (blue) or EN 60S (purple) based on their relative 2DTM SNRs.