Extended Data Fig. 9: Analysis of TREX-pairs on mRNPs.

a. Real-space representation of aligned TREX pairs (n = 275) shown from two views. The reference TREX (TREX-A) is shown as a ribbon representation, and all TREX-Bs are shown as a sphere placed at the TREX-B center. Spheres are colored by TREX-A to -B distances. b. Projection of TREX-B coordinates onto a 2D plane, colored as in A. θ and φ describe the angular component of a vector connecting TREX-A with TREX-B. c. Heatmap of TREX–TREX positions (expressed as θ and φ). d. Violin plot of TREX-A–TREX-B distances, measured from center-to-center or between the two closest atoms. e. Violin plot of rotation angles around the X, Y and Z axis that would align TREX-A with TREX-B. f. Violin plot of TREX mRNP particle volumes measured for particles with more than two TREX complexes per mRNP in our stringently classified dataset or of random TREX–mRNP particles. No significant difference was found (Welch’s t-test, p = 0.0874). g. Violin plot of TREX mRNP particle sphericity measured for particles with more than two TREX complexes per mRNP in our stringently classified dataset or of random TREX–mRNP particles. No significant difference was found (Welch’s t-test, p = 0.3162). h. Scatter plot of TREX–mRNP volume versus sphericity (n = 323). i. Analysis of TREX-A to -B contacts (defined as atoms of TREX-A within 10Å to TREX-B) as observed for TREX pairs on endogenous mRNPs. TREX residues are colored by their proximity frequency, with atoms never in proximity to TREX-B in blue-green and atoms frequently in proximity in bright yellow. j. Analysis of THO–UAP56 contact sites (defined as atoms of THO–UAP56-A within 10 Å to THO–UAP56-B) as observed for the in vitro THO–UAP56 structure²⁷. Atoms within 15 Å to the second copy are colored bright yellow.